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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Muñoz Gomez M, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. Cell Stem Cell 2024; 31:1038-1057.e11. [PMID: 38733993 DOI: 10.1016/j.stem.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/17/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Enteroendocrine cells (EECs) secrete serotonin (enterochromaffin [EC] cells) or specific peptide hormones (non-EC cells) that serve vital metabolic functions. The basis for terminal EEC diversity remains obscure. By forcing activity of the transcription factor (TF) NEUROG3 in 2D cultures of human intestinal stem cells, we replicated physiologic EEC differentiation and examined transcriptional and cis-regulatory dynamics that culminate in discrete cell types. Abundant EEC precursors expressed stage-specific genes and TFs. Before expressing pre-terminal NEUROD1, post-mitotic precursors oscillated between transcriptionally distinct ASCL1+ and HES6hi cell states. Loss of either factor accelerated EEC differentiation substantially and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and non-EC cell features. These TFs mainly bind cis-elements that are accessible in undifferentiated stem cells, and they tailor subsequent expression of TF combinations that underlie discrete EEC identities. Thus, early TF oscillations retard EEC maturation to enable accurate diversity within a medically important cell lineage.
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Affiliation(s)
- Pratik N P Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Wei Gu
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shariq Madha
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Allen W Lynch
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Paloma Cejas
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Ruiyang He
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Swarnabh Bhattacharya
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Miguel Muñoz Gomez
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Qiao Zhou
- Division of Regenerative Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Ramesh A Shivdasani
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Departments of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
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Berthier A, Gheeraert C, Johanns M, Vinod M, Staels B, Eeckhoute J, Lefebvre P. The Molecular Circadian Clock Is a Target of Anti-cancer Translation Inhibitors. J Biol Rhythms 2024; 39:20-34. [PMID: 37872767 DOI: 10.1177/07487304231202561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Circadian-paced biological processes are key to physiology and required for metabolic, immunologic, and cardiovascular homeostasis. Core circadian clock components are transcription factors whose half-life is precisely regulated, thereby controlling the intrinsic cellular circadian clock. Genetic disruption of molecular clock components generally leads to marked pathological events phenotypically affecting behavior and multiple aspects of physiology. Using a transcriptional signature similarity approach, we identified anti-cancer protein synthesis inhibitors as potent modulators of the cardiomyocyte molecular clock. Eukaryotic protein translation inhibitors, ranging from translation initiation (rocaglates, 4-EGI1, etc.) to ribosomal elongation inhibitors (homoharringtonine, puromycin, etc.), were found to potently ablate protein abundance of REV-ERBα, a repressive nuclear receptor and component of the molecular clock. These inhibitory effects were observed both in vitro and in vivo and could be extended to PER2, another component of the molecular clock. Taken together, our observations suggest that the activity spectrum of protein synthesis inhibitors, whose clinical use is contemplated not only in cancers but also in viral infections, must be extended to circadian rhythm disruption, with potential beneficial or iatrogenic effects upon acute or prolonged administration.
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Affiliation(s)
- Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Manuel Johanns
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Manjula Vinod
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille, France
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3
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Singh PNP, Gu W, Madha S, Lynch AW, Cejas P, He R, Bhattacharya S, Gomez MM, Oser MG, Brown M, Long HW, Meyer CA, Zhou Q, Shivdasani RA. Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574746. [PMID: 38260422 PMCID: PMC10802488 DOI: 10.1101/2024.01.09.574746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Enteroendocrine cells (EECs), which secrete serotonin (enterochromaffin cells, EC) or a dominant peptide hormone, serve vital physiologic functions. As with any adult human lineage, the basis for terminal cell diversity remains obscure. We replicated human EEC differentiation in vitro , mapped transcriptional and chromatin dynamics that culminate in discrete cell types, and studied abundant EEC precursors expressing selected transcription factors (TFs) and gene programs. Before expressing the pre-terminal factor NEUROD1, non-replicating precursors oscillated between epigenetically similar but transcriptionally distinct ASCL1 + and HES6 hi cell states. Loss of either factor substantially accelerated EEC differentiation and disrupted EEC individuality; ASCL1 or NEUROD1 deficiency had opposing consequences on EC and hormone-producing cell features. Expressed late in EEC differentiation, the latter TFs mainly bind cis -elements that are accessible in undifferentiated stem cells and tailor the subsequent expression of TF combinations that specify EEC types. Thus, TF oscillations retard EEC maturation to enable accurate EEC diversification.
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4
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Zhang Y, Yan Z, Nan N, Qin G, Sang N. Circadian rhythm disturbances involved in ozone-induced glucose metabolism disorder in mouse liver. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167316. [PMID: 37742977 DOI: 10.1016/j.scitotenv.2023.167316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Ozone (O3) is a key environmental factor for developing diabetes. Nevertheless, the underlying mechanisms remain unclear. This study aimed to investigate alterations of glycometabolism in mice after O3 exposure and the role of circadian rhythms in this process. C57BL/6 male mice were randomly assigned to O3 (0.5 ppm) or filtered air for four weeks (4 h/day). Then, hepatic tissues of mice were collected at 4 h intervals within 24 h after O3 exposure to test. The results showed that hepatic circadian rhythm genes oscillated abnormally, mainly at zeitgeber time (ZT)8 and ZT20 after O3 exposure. Furthermore, detection of glycometabolism (metabolites, enzymes, and genes) revealed that O3 caused change in the daily oscillations of glycometabolism. The serum glucose content decreased at ZT4 and ZT20, while hepatic glucose enhanced at ZT16 and ZT24(0). Both G6pc and Pck1, which are associated with hepatic gluconeogenesis, significantly increased at ZT20. O3 exposure disrupted glycometabolism by increasing gluconeogenesis and decreasing glycolysis in mice liver. Finally, correlation analysis showed that the association between Bmal1 and O3-induced disruption of glycometabolism was the strongest. The findings emphasized the interaction between adverse outcomes of circadian rhythms and glycometabolism following O3 exposure.
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Affiliation(s)
- Yaru Zhang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Zhipeng Yan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Nan Nan
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
| | - Guohua Qin
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, People's Republic of China
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Chamorro R, Jouffe C, Oster H, Uhlenhaut NH, Meyhöfer SM. When should I eat: A circadian view on food intake and metabolic regulation. Acta Physiol (Oxf) 2023; 237:e13936. [PMID: 36645134 DOI: 10.1111/apha.13936] [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: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/11/2023] [Indexed: 01/17/2023]
Abstract
The circadian clock is a hierarchical timing system regulating most physiological and behavioral functions with a period of approximately 24 h in humans and other mammalian species. The circadian clock drives daily eating rhythms that, in turn, reinforce the circadian clock network itself to anticipate and orchestrate metabolic responses to food intake. Eating is tightly interconnected with the circadian clock and recent evidence shows that the timing of meals is crucial for the control of appetite and metabolic regulation. Obesity results from combined long-term dysregulation in food intake (homeostatic and hedonic circuits), energy expenditure, and energy storage. Increasing evidence supports that the loss of synchrony of daily rhythms significantly impairs metabolic homeostasis and is associated with obesity. This review presents an overview of mechanisms regulating food intake (homeostatic/hedonic) and focuses on the crucial role of the circadian clock on the metabolic response to eating, thus providing a fundamental research axis to maintain a healthy eating behavior.
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Affiliation(s)
- Rodrigo Chamorro
- Institute for Endocrinology and Diabetes, University of Lübeck, Lübeck, Germany.,Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Céline Jouffe
- Institute for Diabetes and Endocrinology, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany.,Institute for Diabetes and Cancer, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Henrik Oster
- Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany.,Institute of Neurobiology, University of Lübeck, Lübeck, Germany
| | - N Henriette Uhlenhaut
- Institute for Diabetes and Endocrinology, Helmholtz Diabetes Center, Helmholtz Zentrum München, Neuherberg, Germany.,Chair for Metabolic Programming, TUM School of Life Sciences Weihenstephan, & ZIEL-Institute for Food & Health, Freising, Germany
| | - Sebastian M Meyhöfer
- Institute for Endocrinology and Diabetes, University of Lübeck, Lübeck, Germany.,Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
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6
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Kelliher CM, Stevenson EL, Loros JJ, Dunlap JC. Nutritional compensation of the circadian clock is a conserved process influenced by gene expression regulation and mRNA stability. PLoS Biol 2023; 21:e3001961. [PMID: 36603054 PMCID: PMC9848017 DOI: 10.1371/journal.pbio.3001961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 01/18/2023] [Accepted: 12/15/2022] [Indexed: 01/06/2023] Open
Abstract
Compensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator's period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured human cells, we selected top hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian orthologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down the mammalian orthologs of the Neurospora compensation-associated genes CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.
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Affiliation(s)
- Christina M. Kelliher
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
- Department of Biology, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Elizabeth-Lauren Stevenson
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jennifer J. Loros
- Department of Biochemistry & Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Jay C. Dunlap
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
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7
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Uehara TN, Nonoyama T, Taki K, Kuwata K, Sato A, Fujimoto KJ, Hirota T, Matsuo H, Maeda AE, Ono A, Takahara TT, Tsutsui H, Suzuki T, Yanai T, Kay SA, Itami K, Kinoshita T, Yamaguchi J, Nakamichi N. Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period. PLANT & CELL PHYSIOLOGY 2022; 63:450-462. [PMID: 35086143 PMCID: PMC9016870 DOI: 10.1093/pcp/pcac011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.
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Affiliation(s)
| | | | | | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Kazuhiro J Fujimoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Hiromi Matsuo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Akari E Maeda
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Azusa Ono
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Tomoaki T Takahara
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Hiroki Tsutsui
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, 487-8501 Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA 90033, USA
| | - Kenichiro Itami
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
- JST ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Junichiro Yamaguchi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
| | - Norihito Nakamichi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
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8
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Core clock regulators in dexamethasone-treated HEK 293T cells at 4 h intervals. BMC Res Notes 2022; 15:23. [PMID: 35090555 PMCID: PMC8796574 DOI: 10.1186/s13104-021-05871-7] [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: 09/14/2021] [Accepted: 11/30/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The study of the circadian clock and its mechanisms is easily facilitated through clock resetting in cell culture. Among the various established synchronizers of the circadian clock in cell culture (temperature, serum shock, glucocorticoids), the artificial glucocorticoid Dexamethasone (DEX) is the most widely used. DEX treatment as a protocol to reset the circadian clock in culture gives simple readout with minimal laboratory requirements. Even though there are many studies regarding clock resetting in culture using DEX, reference points or expression patterns of core clock genes and their protein products are scarce and sometimes contradict other works with similar methodology. We synchronise a cell line of human origin with DEX to be used for studies on circadian rhythms. RESULTS We treat HEK 293T cells with DEX and describe the patterns of mRNA and proteins of core clock regulators, while making a clear point on how CLOCK is less than an ideal molecule to help monitor rhythms in this cell line.
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Wong DCS, Seinkmane E, Zeng A, Stangherlin A, Rzechorzek NM, Beale AD, Day J, Reed M, Peak‐Chew SY, Styles CT, Edgar RS, Putker M, O’Neill JS. CRYPTOCHROMES promote daily protein homeostasis. EMBO J 2022; 41:e108883. [PMID: 34842284 PMCID: PMC8724739 DOI: 10.15252/embj.2021108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
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Affiliation(s)
| | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | | | - Jason Day
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Martin Reed
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Rachel S Edgar
- Department of Infectious DiseasesImperial CollegeLondonUK
| | - Marrit Putker
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Crown BioscienceUtrechtthe Netherlands
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10
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Kim R, Witelski TP. Uncovering the dynamics of a circadian-dopamine model influenced by the light-dark cycle. Math Biosci 2021; 344:108764. [PMID: 34952036 DOI: 10.1016/j.mbs.2021.108764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
The neurotransmitter dopamine (DA) is known to be influenced by the circadian timekeeping system in the mammalian brain. We have previously created a single-cell differential equations model to understand the mechanisms behind circadian rhythms of extracellular DA. In this paper, we investigate the dynamics in our model and study different behaviors such as entrainment to the 24-hour light-dark cycle and robust periodicity versus decoupling, quasiperiodicity, and chaos. Imbalances in DA are often accompanied by disrupted circadian rhythms, such as in Parkinson's disease, hyperactivity, and mood disorders. Our model provides new insights into the links between the circadian clock and DA. We show that the daily rhythmicity of DA can be disrupted by decoupling between interlocked loops of the clock circuitry or by quasiperiodic clock behaviors caused by misalignment with the light-dark cycle. The model can be used to further study how the circadian clock affects the dopaminergic system, and to help develop therapeutic strategies for disrupted DA rhythms. .
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Affiliation(s)
- Ruby Kim
- Department of Mathematics, Duke University, Durham, NC, USA.
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11
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Krylov VV, Izvekov EI, Pavlova VV, Pankova NA, Osipova EA. Circadian rhythms in zebrafish (Danio rerio) behaviour and the sources of their variability. Biol Rev Camb Philos Soc 2020; 96:785-797. [PMID: 33331134 DOI: 10.1111/brv.12678] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022]
Abstract
Over recent decades, changes in zebrafish (Danio rerio) behaviour have become popular quantitative indicators in biomedical studies. The circadian rhythms of behavioural processes in zebrafish are known to enable effective utilization of energy and resources, therefore attracting interest in zebrafish as a research model. This review covers a variety of circadian behaviours in this species, including diurnal rhythms of spawning, feeding, locomotor activity, shoaling, light/dark preference, and vertical position preference. Changes in circadian activity during zebrafish ontogeny are reviewed, including ageing-related alterations and chemically induced variations in rhythmicity patterns. Both exogenous and endogenous sources of inter-individual variability in zebrafish circadian behaviour are detailed. Additionally, we focus on different environmental factors with the potential to entrain circadian processes in zebrafish. This review describes two principal ways whereby diurnal behavioural rhythms can be entrained: (i) modulation of organismal physiological state, which can have masking or enhancing effects on behavioural endpoints related to endogenous circadian rhythms, and (ii) modulation of period and amplitude of the endogenous circadian rhythm due to competitive relationships between the primary and secondary zeitgebers. In addition, different peripheral oscillators in zebrafish can be entrained by diverse zeitgebers. This complicated orchestra of divergent influences may cause variability in zebrafish circadian behaviours, which should be given attention when planning behavioural studies.
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Affiliation(s)
- Viacheslav V Krylov
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Nekouz, Yaroslavl Oblast, 152742, Russia
| | - Evgeny I Izvekov
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Nekouz, Yaroslavl Oblast, 152742, Russia
| | - Vera V Pavlova
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Nekouz, Yaroslavl Oblast, 152742, Russia
| | - Natalia A Pankova
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Nekouz, Yaroslavl Oblast, 152742, Russia
| | - Elena A Osipova
- I.D. Papanin Institute for Biology of Inland Waters Russian Academy of Sciences, Borok, Nekouz, Yaroslavl Oblast, 152742, Russia
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12
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Dibner C. The importance of being rhythmic: Living in harmony with your body clocks. Acta Physiol (Oxf) 2020; 228:e13281. [PMID: 30980501 DOI: 10.1111/apha.13281] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Abstract
Circadian rhythms have developed in all light-sensitive organisms, including humans, as a fundamental anticipatory mechanism that enables proactive adaptation to environmental changes. The circadian system is organized in a highly hierarchical manner, with clocks operative in most cells of the body ensuring the temporal coordination of physiological processes. Circadian misalignment, stemming from modern life style, draws increasing attention due to its tight association with the development of metabolic, cardiovascular, inflammatory and mental diseases as well as cancer. This review highlights recent findings emphasizing the role of the circadian system in the temporal orchestration of physiology, with a particular focus on implications of circadian misalignment in human pathologies.
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Affiliation(s)
- Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Medicine University Hospital of Geneva Geneva Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine University of Geneva Geneva Switzerland
- Diabetes Center, Faculty of Medicine University of Geneva Geneva Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3) Geneva Switzerland
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13
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Guo G, Wang K, Hu SS, Tian T, Liu P, Mori T, Chen P, Johnson CH, Qin X. Autokinase Activity of Casein Kinase 1 δ/ε Governs the Period of Mammalian Circadian Rhythms. J Biol Rhythms 2019; 34:482-496. [PMID: 31392916 DOI: 10.1177/0748730419865406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Circadian rhythms exist in nearly all organisms. In mammals, transcriptional and translational feedback loops (TTFLs) are believed to underlie the mechanism of the circadian clock. Casein kinase 1δ/ε (CK1δ/ε) are key kinases that phosphorylate clock components such as PER proteins, determining the pace of the clock. Most previous studies of the biochemical properties of the key kinases CK1ε and CK1δ in vitro have focused on the properties of the catalytic domains from which the autoinhibitory C-terminus has been deleted (ΔC); those studies ignored the significance of self-inhibition by autophosphorylation. By comparing the properties of the catalytic domain of CK1δ/ε with the full-length kinase that can undergo autoinhibition, we found that recombinant full-length CK1 showed a sequential autophosphorylation process that induces conformational changes to affect the overall kinase activity. Furthermore, a direct relationship between the period change and the autokinase activity among CK1δ, CK1ε, and CK1ε-R178C was observed. These data implicate the autophosphorylation activity of CK1δ and CK1ε kinases in setting the pace of mammalian circadian rhythms and indicate that the circadian period can be modulated by tuning the autophosphorylation rates of CK1δ/ε.
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Affiliation(s)
- Gaili Guo
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Kankan Wang
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Shan-Shan Hu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Tian Tian
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Peng Liu
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Tetsuya Mori
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Peng Chen
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | | | - Ximing Qin
- Department of Health Sciences, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
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14
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Nieto PS, Condat CA. Translational thresholds in a core circadian clock model. Phys Rev E 2019; 100:022409. [PMID: 31574627 DOI: 10.1103/physreve.100.022409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Indexed: 06/10/2023]
Abstract
Organisms have evolved in a daily cyclic environment, developing circadian cell-autonomous clocks that temporally organize a wide range of biological processes. Translation is a highly regulated process mainly associated with the activity of microRNAs (miRNAs) at the translation initiation step that impacts on the molecular circadian clock dynamics. Recently, a molecular titration mechanism was proposed to explain the interactions between some miRNAs and their target mRNAs; new evidence also indicates that regulation by miRNA is a nonlinear process such that there is a threshold level of target mRNA below which protein production is drastically repressed. These observations led us to use a theoretical model of the circadian molecular clock to study the effect of miRNA-mediated translational thresholds on the molecular clock dynamics. We model the translational threshold by introducing a phenomenological Hill equation for the kinetics of PER translation and show how the parameters associated with translation kinetics affect the period, amplitude, and time delays between clock mRNA and clock protein expression. We show that our results are useful for analyzing experiments related to the translational regulation of negative elements of transcriptional-translational feedback loops. We also provide new elements for thinking about the translational threshold as a mechanism that favors the emergence of circadian rhythmicity, the tuning of the period-delay relationship and the cell capacity to control the protein oscillation amplitude with almost negligible changes in the mRNA amplitudes.
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Affiliation(s)
- Paula S Nieto
- Instituto de Física Enrique Gaviola (IFEG)-CONICET and Facultad de Matemática, Astronomía, Física y Computación, Universidad Nacional de Córdoba, Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - C A Condat
- Instituto de Física Enrique Gaviola (IFEG)-CONICET and Facultad de Matemática, Astronomía, Física y Computación, Universidad Nacional de Córdoba, Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
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15
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Xie Y, Tang Q, Chen G, Xie M, Yu S, Zhao J, Chen L. New Insights Into the Circadian Rhythm and Its Related Diseases. Front Physiol 2019; 10:682. [PMID: 31293431 PMCID: PMC6603140 DOI: 10.3389/fphys.2019.00682] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms (CR) are a series of endogenous autonomous oscillators generated by the molecular circadian clock which acting on coordinating internal time with the external environment in a 24-h daily cycle. The circadian clock system is a major regulatory factor for nearly all physiological activities and its disorder has severe consequences on human health. CR disruption is a common issue in modern society, and researches about people with jet lag or shift works have revealed that CR disruption can cause cognitive impairment, psychiatric illness, metabolic syndrome, dysplasia, and cancer. In this review, we summarized the synchronizers and the synchronization methods used in experimental research, and introduced CR monitoring and detection methods. Moreover, we evaluated conventional CR databases, and analyzed experiments that characterized the underlying causes of CR disorder. Finally, we further discussed the latest developments in understanding of CR disruption, and how it may be relevant to health and disease. Briefly, this review aimed to synthesize previous studies to aid in future studies of CR and CR-related diseases.
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Affiliation(s)
- Yanling Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangjin Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengru Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaoling Yu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajia Zhao
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Upadhyay A, Brunner M, Herzel H. An Inactivation Switch Enables Rhythms in a Neurospora Clock Model. Int J Mol Sci 2019; 20:E2985. [PMID: 31248072 PMCID: PMC6627049 DOI: 10.3390/ijms20122985] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 12/17/2022] Open
Abstract
Autonomous endogenous time-keeping is ubiquitous across many living organisms, known as the circadian clock when it has a period of about 24 h. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungus Neurospora crassa is a well-established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock of Neurospora is composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex, which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics, we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedback among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 h. Our model reveals a switch between WC1-induced transcription and FFC-assisted inactivation of WC1. Using the new model, we also study the possible mechanisms of glucose compensation. A fairly simple model with just three nonlinearities helps to elucidate clock dynamics, revealing a mechanism of rhythms' production. The model can further be utilized to study entrainment and temperature compensation.
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Affiliation(s)
- Abhishek Upadhyay
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin and Humboldt University of Berlin, Philippstr. 13, 10115 Berlin, Germany.
| | - Michael Brunner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin and Humboldt University of Berlin, Philippstr. 13, 10115 Berlin, Germany.
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17
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Beale AD, Kruchek E, Kitcatt SJ, Henslee EA, Parry JS, Braun G, Jabr R, von Schantz M, O’Neill JS, Labeed FH. Casein Kinase 1 Underlies Temperature Compensation of Circadian Rhythms in Human Red Blood Cells. J Biol Rhythms 2019; 34:144-153. [PMID: 30898060 PMCID: PMC6458989 DOI: 10.1177/0748730419836370] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Temperature compensation and period determination by casein kinase 1 (CK1) are conserved features of eukaryotic circadian rhythms, whereas the clock gene transcription factors that facilitate daily gene expression rhythms differ between phylogenetic kingdoms. Human red blood cells (RBCs) exhibit temperature-compensated circadian rhythms, which, because RBCs lack nuclei, must occur in the absence of a circadian transcription-translation feedback loop. We tested whether period determination and temperature compensation are dependent on CKs in RBCs. As with nucleated cell types, broad-spectrum kinase inhibition with staurosporine lengthened the period of the RBC clock at 37°C, with more specific inhibition of CK1 and CK2 also eliciting robust changes in circadian period. Strikingly, inhibition of CK1 abolished temperature compensation and increased the Q10 for the period of oscillation in RBCs, similar to observations in nucleated cells. This indicates that CK1 activity is essential for circadian rhythms irrespective of the presence or absence of clock gene expression cycles.
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Affiliation(s)
- Andrew D. Beale
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Emily Kruchek
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Stephen J. Kitcatt
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Erin A. Henslee
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Jack S.W. Parry
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Gabriella Braun
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Rita Jabr
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - Malcolm von Schantz
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, UK
| | - John S. O’Neill
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Fatima H. Labeed
- Faculty of Engineering and Physical Sciences, University of Surrey, Guildford, Surrey, UK
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18
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Gibo S, Kurosawa G. Non-sinusoidal Waveform in Temperature-Compensated Circadian Oscillations. Biophys J 2019; 116:741-751. [PMID: 30712786 DOI: 10.1016/j.bpj.2018.12.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/04/2018] [Accepted: 12/28/2018] [Indexed: 10/27/2022] Open
Abstract
Time series of biological rhythms are of various shapes. Here, we investigated the waveforms of circadian rhythms in gene-protein dynamics using a newly developed, to our knowledge, index to quantify the degree of distortion from a sinusoidal waveform. In general, most biochemical reactions accelerate with increasing temperature, but the period of circadian rhythms remains relatively stable with temperature change, a phenomenon known as "temperature compensation." Despite extensive research, the mechanism underlying this remains unclear. To understand the mechanism, we used transcriptional-translational oscillator models for circadian rhythms in the fruit fly Drosophila and mammals. Given the assumption that reaction rates increase with temperature, mathematical analyses revealed that temperature compensation required waveforms that are more nonsinusoidal at higher temperatures. We then analyzed a post-translational oscillator (PTO) model of cyanobacteria circadian rhythms. Because the structure of the PTO is different from that of the transcriptional-translational oscillator, the condition for temperature compensation would be expected to differ. Unexpectedly, the computational analysis again showed that temperature compensation in the PTO model required a more nonsinusoidal waveform at higher temperatures. This finding held for both models even with a milder assumption that some reaction rates do not change with temperature, which is consistent with experimental evidence. Together, our theoretical analyses predict that the waveform of circadian gene-activity and/or protein phosphorylation rhythms would be more nonsinusoidal at higher temperatures, even when there are differences in the network structures.
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Affiliation(s)
- Shingo Gibo
- Interdisciplinary Theoretical and Mathematical Sciences Program, RIKEN, Wako, Japan.
| | - Gen Kurosawa
- Interdisciplinary Theoretical and Mathematical Sciences Program, RIKEN, Wako, Japan; Theoretical Biology Laboratory, RIKEN, Wako, Japan
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19
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Causton HC. Metabolic rhythms: A framework for coordinating cellular function. Eur J Neurosci 2018; 51:1-12. [PMID: 30548718 DOI: 10.1111/ejn.14296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]
Abstract
Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.
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Affiliation(s)
- Helen C Causton
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, New York
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20
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Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock. Biophys J 2018; 115:2055-2066. [PMID: 30473017 DOI: 10.1016/j.bpj.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/29/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
Mathematical models of fundamental biological processes play an important role in consolidating theory and experiments, especially if they are systematically developed, thoroughly characterized, and well tested by experimental data. In this work, we report a detailed bifurcation analysis of a mathematical model of the mammalian circadian clock network developed by Relógio et al., noteworthy for its consistency with available data. Using one- and two-parameter bifurcation diagrams, we explore how oscillations in the model depend on the expression levels of its constituent genes and the activities of their encoded proteins. These bifurcation diagrams allow us to decipher the dynamics of interlocked feedback loops by parametric variation of genes and proteins in the model. Among other results, we find that REV-ERB, a member of a subfamily of orphan nuclear receptors, plays a critical role in the intertwined dynamics of Relógio's model. The bifurcation diagrams reported here can be used for predicting how the core clock network responds-in terms of period, amplitude and phases of oscillations-to different perturbations.
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21
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Wong DCS, O’Neill JS. Non-transcriptional processes in circadian rhythm generation. CURRENT OPINION IN PHYSIOLOGY 2018; 5:117-132. [PMID: 30596188 PMCID: PMC6302373 DOI: 10.1016/j.cophys.2018.10.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
'Biological clocks' orchestrate mammalian biology to a daily rhythm. Whilst 'clock gene' transcriptional circuits impart rhythmic regulation to myriad cellular systems, our picture of the biochemical mechanisms that determine their circadian (∼24 hour) period is incomplete. Here we consider the evidence supporting different models for circadian rhythm generation in mammalian cells in light of evolutionary factors. We find it plausible that the circadian timekeeping mechanism in mammalian cells is primarily protein-based, signalling biological timing information to the nucleus by the post-translational regulation of transcription factor activity, with transcriptional feedback imparting robustness to the oscillation via hysteresis. We conclude by suggesting experiments that might distinguish this model from competing paradigms.
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22
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Petrenko V, Philippe J, Dibner C. Time zones of pancreatic islet metabolism. Diabetes Obes Metab 2018; 20 Suppl 2:116-126. [PMID: 30230177 DOI: 10.1111/dom.13383] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 05/04/2018] [Accepted: 05/23/2018] [Indexed: 12/28/2022]
Abstract
Most living beings possess an intrinsic system of circadian oscillators, allowing anticipation of the Earth's rotation around its own axis. The mammalian circadian timing system orchestrates nearly all aspects of physiology and behaviour. Together with systemic signals originating from the central clock that resides in the hypothalamic suprachiasmatic nucleus, peripheral oscillators orchestrate tissue-specific fluctuations in gene transcription and translation, and posttranslational modifications, driving overt rhythms in physiology and behaviour. There is accumulating evidence of a reciprocal connection between the circadian oscillator and most aspects of physiology and metabolism, in particular as the circadian system plays a critical role in orchestrating body glucose homeostasis. Recent reports imply that circadian clocks operative in the endocrine pancreas regulate insulin secretion, and that islet clock perturbation in rodents leads to the development of overt type 2 diabetes. While whole islet clocks have been extensively studied during the last years, the heterogeneity of islet cell oscillators and the interplay between α- and β-cellular clocks for orchestrating glucagon and insulin secretion have only recently gained attention. Here, we review recent findings on the molecular makeup of the circadian clocks operative in pancreatic islet cells in rodents and in humans, and focus on the physiologically relevant synchronizers that are resetting these time-keepers. Moreover, the implication of islet clock functional outputs in the temporal coordination of metabolism in health and disease will be highlighted.
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Affiliation(s)
- Volodymyr Petrenko
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Jacques Philippe
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
| | - Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics in Geneva (iGE3), Geneva, Switzerland
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23
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Ode KL, Ueda HR. Design Principles of Phosphorylation-Dependent Timekeeping in Eukaryotic Circadian Clocks. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a028357. [PMID: 29038116 DOI: 10.1101/cshperspect.a028357] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The circadian clock in cyanobacteria employs a posttranslational oscillator composed of a sequential phosphorylation-dephosphorylation cycle of KaiC protein, in which the dynamics of protein structural changes driven by temperature-compensated KaiC's ATPase activity are critical for determining the period. On the other hand, circadian clocks in eukaryotes employ transcriptional feedback loops as a core mechanism. In this system, the dynamics of protein accumulation and degradation affect the circadian period. However, recent studies of eukaryotic circadian clocks reveal that the mechanism controlling the circadian period can be independent of the regulation of protein abundance. Instead, the circadian substrate is often phosphorylated at multiple sites at flexible protein regions to induce structural changes. The phosphorylation is catalyzed by kinases that induce sequential multisite phosphorylation such as casein kinase 1 (CK1) with temperature-compensated activity. We propose that the design principles of phosphorylation-dependent circadian-period determination in eukaryotes may share characteristics with the posttranslational oscillator in cyanobacteria.
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Affiliation(s)
- Koji L Ode
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.,Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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24
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Green CB. Circadian Posttranscriptional Regulatory Mechanisms in Mammals. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a030692. [PMID: 28778869 DOI: 10.1101/cshperspect.a030692] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The circadian clock drives rhythms in the levels of thousands of proteins in the mammalian cell, arising in part from rhythmic transcriptional regulation of the genes that encode them. However, recent evidence has shown that posttranscriptional processes also play a major role in generating the rhythmic protein makeup and ultimately the rhythmic physiology of the cell. Regulation of steps throughout the life of the messenger RNA (mRNA), ranging from initial mRNA processing and export from the nucleus to extensive control of translation and degradation in the cytosol have been shown to be important for producing the final rhythms in protein levels critical for proper circadian rhythmicity. These findings will be reviewed here.
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Affiliation(s)
- Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9111
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25
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Tainaka M, Doi M, Inoue Y, Murai I, Okamura H. Circadian PER2 protein oscillations do not persist in cycloheximide-treated mouse embryonic fibroblasts in culture. Chronobiol Int 2017; 35:132-136. [PMID: 29283306 DOI: 10.1080/07420528.2017.1316731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
It is not known whether the endogenous mammalian core clock proteins sustain measurable oscillations in cells in culture where de novo translation is pharmacologically inhibited. We studied here the mammalian core clock protein PER2, which undergoes robust circadian oscillations in both abundance and phosphorylation. With a newly developed antibody that enables tracing the endogenous PER2 protein oscillations over circadian cycles with cultured mouse embryonic fibroblast cells, we provide evidence that PER2 does not persist noticeable circadian rhythms when translation is inhibited.
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Affiliation(s)
- Motomi Tainaka
- a Department of Systems Biology, Graduate School of Pharmaceutical Sciences , Kyoto University , Kyoto , Japan
| | - Masao Doi
- a Department of Systems Biology, Graduate School of Pharmaceutical Sciences , Kyoto University , Kyoto , Japan
| | - Yuichi Inoue
- a Department of Systems Biology, Graduate School of Pharmaceutical Sciences , Kyoto University , Kyoto , Japan
| | - Iori Murai
- a Department of Systems Biology, Graduate School of Pharmaceutical Sciences , Kyoto University , Kyoto , Japan
| | - Hitoshi Okamura
- a Department of Systems Biology, Graduate School of Pharmaceutical Sciences , Kyoto University , Kyoto , Japan
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26
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Myung J, Pauls SD. Encoding seasonal information in a two-oscillator model of the multi-oscillator circadian clock. Eur J Neurosci 2017; 48:2718-2727. [PMID: 28921823 DOI: 10.1111/ejn.13697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/01/2017] [Accepted: 09/11/2017] [Indexed: 02/01/2023]
Abstract
The suprachiasmatic nucleus (SCN) is a collection of about 10 000 neurons, each of which functions as a circadian clock with slightly different periods and phases, that work in concert with form and maintain the master circadian clock for the organism. The diversity among neurons confers on the SCN the ability to robustly encode both the 24-h light pattern as well as the seasonal time. Cluster synchronization brings the different neurons into line and reduces the large population to essentially two oscillators, coordinated by a macroscopic network motif of asymmetric repulsive-attractive coupling. We recount the steps leading to this simplification and rigorously examine the two-oscillator case by seeking an analytical solution. Through these steps, we identify physiologically relevant parameters that shape the behaviour of the SCN network and delineate its ability to store past details of seasonal variation in photoperiod.
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Affiliation(s)
- Jihwan Myung
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Lab 2 Level B, 1919-1 Tancha Onna-son, Kunigami, Okinawa 904-0495, Japan.,Graduate Institute of Humanities in Medicine, Taipei Medical University, Taipei, Taiwan.,TMU-Research Center of Brain and Consciousness, Shuang Ho Hospital, New Taipei City, Taiwan
| | - Scott D Pauls
- Department of Mathematics, Dartmouth College, 6188 Kemeny Hall, Hanover, NH 03755, USA
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27
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Temperature-amplitude coupling for stable biological rhythms at different temperatures. PLoS Comput Biol 2017; 13:e1005501. [PMID: 28594845 PMCID: PMC5464531 DOI: 10.1371/journal.pcbi.1005501] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/03/2017] [Indexed: 11/19/2022] Open
Abstract
Most biological processes accelerate with temperature, for example cell division. In contrast, the circadian rhythm period is robust to temperature fluctuation, termed temperature compensation. Temperature compensation is peculiar because a system-level property (i.e., the circadian period) is stable under varying temperature while individual components of the system (i.e., biochemical reactions) are usually temperature-sensitive. To understand the mechanism for period stability, we measured the time series of circadian clock transcripts in cultured C6 glioma cells. The amplitudes of Cry1 and Dbp circadian expression increased significantly with temperature. In contrast, other clock transcripts demonstrated no significant change in amplitude. To understand these experimental results, we analyzed mathematical models with different network topologies. It was found that the geometric mean amplitude of gene expression must increase to maintain a stable period with increasing temperatures and reaction speeds for all models studied. To investigate the generality of this temperature-amplitude coupling mechanism for period stability, we revisited data on the yeast metabolic cycle (YMC) period, which is also stable under temperature variation. We confirmed that the YMC amplitude increased at higher temperatures, suggesting temperature-amplitude coupling as a common mechanism shared by circadian and 4 h-metabolic rhythms.
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Gachon F, Loizides-Mangold U, Petrenko V, Dibner C. Glucose Homeostasis: Regulation by Peripheral Circadian Clocks in Rodents and Humans. Endocrinology 2017; 158:1074-1084. [PMID: 28324069 DOI: 10.1210/en.2017-00218] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 03/10/2017] [Indexed: 12/15/2022]
Abstract
Most organisms, including humans, have developed an intrinsic system of circadian oscillators, allowing the anticipation of events related to the rotation of Earth around its own axis. The mammalian circadian timing system orchestrates nearly all aspects of physiology and behavior. Together with systemic signals, emanating from the central clock that resides in the hypothalamus, peripheral oscillators orchestrate tissue-specific fluctuations in gene expression, protein synthesis, and posttranslational modifications, driving overt rhythms in physiology and behavior. There is increasing evidence on the essential roles of the peripheral oscillators, operative in metabolically active organs in the regulation of body glucose homeostasis. Here, we review some recent findings on the molecular and cellular makeup of the circadian timing system and its implications in the temporal coordination of metabolism in health and disease.
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Affiliation(s)
- Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, CH-1015 Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Loizides-Mangold
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, CH-1211 Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Diabetes Center, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Volodymyr Petrenko
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, CH-1211 Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Diabetes Center, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
| | - Charna Dibner
- Division of Endocrinology, Diabetes, Hypertension and Nutrition, Department of Internal Medicine Specialties, University Hospital of Geneva, CH-1211 Geneva, Switzerland
- Department of Cell Physiology and Metabolism, Diabetes Center, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland
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Seasonal loss and resumption of circadian rhythms in hibernating arctic ground squirrels. J Comp Physiol B 2017; 187:693-703. [PMID: 28332018 DOI: 10.1007/s00360-017-1069-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 02/04/2017] [Accepted: 02/26/2017] [Indexed: 12/28/2022]
Abstract
Circadian clocks are near universal among organisms and play a key role in coordinating physiological and metabolic functions to anticipate or coincide with predictable daily changes in the physical and social environment. However, whether circadian rhythms persist and are functionally important during hibernation in all mammals is currently unclear. We examined whether circadian rhythms of body temperature (T b) persist during multi-day, steady-state torpor and investigated the association between timing of animal emergence, exposure to light, and resumption of activity and T b rhythms in free-living and captive male arctic ground squirrels. High-resolution (0.02 °C) temperature loggers revealed that circadian rhythms of T b were not present during deep torpor in free-living arctic ground squirrels. Significant circadian rhythms of T b resumed, however, following the resumption of euthermia, but prior to emergence, though rhythms became much more robust coincident with aboveground emergence. Additionally, squirrels maintained in captivity under conditions of constant darkness spontaneously developed significant circadian rhythms of T b and activity soon after ending torpor. Exposing animals to a 5-s pulse of light within a week when they ended torpor increased the strength of rhythms. Our results are consistent with the hypothesis that circadian clock function is inhibited during hibernation in arctic ground squirrels, and we postulate that exposure to external stimuli, such as light in free-living animals, and meals or acute disturbance for captive squirrels, may enhance T b rhythmicity by synchronizing loosely coupled circadian oscillators within the suprachiasmatic nucleus.
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Abstract
Chronobiological studies of prokaryotic organisms have generally lagged far behind the study of endogenous circadian clocks in eukaryotes, in which such systems are essentially ubiquitous. However, despite only being studied during the past 25 years, cyanobacteria have become important model organisms for the study of circadian rhythms and, presently, their timekeeping mechanism is the best understood of any system in terms of biochemistry, structural biology, biophysics and adaptive importance. Nevertheless, intrinsic daily rhythmicity among bacteria other than cyanobacteria is essentially unknown; some tantalizing information suggests widespread daily timekeeping among Eubacteria and Archaea through mechanisms that share common elements with the cyanobacterial clock but are distinct. Moreover, the recent surge of information about microbiome-host interactions has largely neglected the temporal dimension and yet daily cycles control important aspects of their relationship.
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Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front Neurol 2017; 8:25. [PMID: 28220104 PMCID: PMC5292584 DOI: 10.3389/fneur.2017.00025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms. We review how systems methods have helped to elucidate complex behaviors of the circadian clock including temperature compensation, rhythmicity, and robustness. Finally, we explain the contribution of systems biology to the transcription-translation feedback loop and posttranslational oscillator models of circadian rhythms and describe new technologies and "-omics" approaches to understand circadian timekeeping and neurophysiology.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Atger F, Mauvoisin D, Weger B, Gobet C, Gachon F. Regulation of Mammalian Physiology by Interconnected Circadian and Feeding Rhythms. Front Endocrinol (Lausanne) 2017; 8:42. [PMID: 28337174 PMCID: PMC5340782 DOI: 10.3389/fendo.2017.00042] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/17/2017] [Indexed: 12/29/2022] Open
Abstract
Circadian clocks are endogenous timekeeping systems that adapt in an anticipatory fashion the physiology and behavior of most living organisms. In mammals, the master pacemaker resides in the suprachiasmatic nucleus and entrains peripheral clocks using a wide range of signals that differentially schedule physiology and gene expression in a tissue-specific manner. The peripheral clocks, such as those found in the liver, are particularly sensitive to rhythmic external cues like feeding behavior, which modulate the phase and amplitude of rhythmic gene expression. Consequently, the liver clock temporally tunes the expression of many genes involved in metabolism and physiology. However, the circadian modulation of cellular functions also relies on multiple layers of posttranscriptional and posttranslational regulation. Strikingly, these additional regulatory events may happen independently of any transcriptional oscillations, showing that complex regulatory networks ultimately drive circadian output functions. These rhythmic events also integrate feeding-related cues and adapt various metabolic processes to food availability schedules. The importance of such temporal regulation of metabolism is illustrated by metabolic dysfunctions and diseases resulting from circadian clock disruption or inappropriate feeding patterns. Therefore, the study of circadian clocks and rhythmic feeding behavior should be of interest to further advance our understanding of the prevention and therapy of metabolic diseases.
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Affiliation(s)
- Florian Atger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- Department of Pharmacology and Toxicology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Mauvoisin
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Benjamin Weger
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
| | - Cédric Gobet
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Frédéric Gachon
- Department of Diabetes and Circadian Rhythms, Nestlé Institute of Health Sciences, Lausanne, Switzerland
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- *Correspondence: Frédéric Gachon,
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Pett JP, Korenčič A, Wesener F, Kramer A, Herzel H. Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator. PLoS Comput Biol 2016; 12:e1005266. [PMID: 27942033 PMCID: PMC5189953 DOI: 10.1371/journal.pcbi.1005266] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 12/27/2016] [Accepted: 11/27/2016] [Indexed: 11/18/2022] Open
Abstract
Mammals evolved an endogenous timing system to coordinate their physiology and behaviour to the 24h period of the solar day. While it is well accepted that circadian rhythms are generated by intracellular transcriptional feedback loops, it is still debated which network motifs are necessary and sufficient for generating self-sustained oscillations. Here, we systematically explore a data-based circadian oscillator model with multiple negative and positive feedback loops and identify a series of three subsequent inhibitions known as "repressilator" as a core element of the mammalian circadian oscillator. The central role of the repressilator motif is consistent with time-resolved ChIP-seq experiments of circadian clock transcription factors and loss of rhythmicity in core clock gene knockouts.
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Affiliation(s)
- J. Patrick Pett
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anja Korenčič
- Center for Functional Genomics and Biochips, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Felix Wesener
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- * E-mail:
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Petrenko V, Saini C, Perrin L, Dibner C. Parallel Measurement of Circadian Clock Gene Expression and Hormone Secretion in Human Primary Cell Cultures. J Vis Exp 2016. [PMID: 27911383 DOI: 10.3791/54673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Circadian clocks are functional in all light-sensitive organisms, allowing for an adaptation to the external world by anticipating daily environmental changes. Considerable progress in our understanding of the tight connection between the circadian clock and most aspects of physiology has been made in the field over the last decade. However, unraveling the molecular basis that underlies the function of the circadian oscillator in humans stays of highest technical challenge. Here, we provide a detailed description of an experimental approach for long-term (2-5 days) bioluminescence recording and outflow medium collection in cultured human primary cells. For this purpose, we have transduced primary cells with a lentiviral luciferase reporter that is under control of a core clock gene promoter, which allows for the parallel assessment of hormone secretion and circadian bioluminescence. Furthermore, we describe the conditions for disrupting the circadian clock in primary human cells by transfecting siRNA targeting CLOCK. Our results on the circadian regulation of insulin secretion by human pancreatic islets, and myokine secretion by human skeletal muscle cells, are presented here to illustrate the application of this methodology. These settings can be used to study the molecular makeup of human peripheral clocks and to analyze their functional impact on primary cells under physiological or pathophysiological conditions.
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Affiliation(s)
- Volodymyr Petrenko
- Department of Medical Specialties, Division of Endocrinology, Diabetes, Hypertension and Nutrition, Diabetes Center, University of Geneva Medical School, Institute of Genetics and Genomics in Geneva (iGE3)
| | - Camille Saini
- Population Epidemiology Unit (UEP), Community Medicine, Geneva University Hospital
| | - Laurent Perrin
- Department of Medical Specialties, Division of Endocrinology, Diabetes, Hypertension and Nutrition, Diabetes Center, University of Geneva Medical School, Institute of Genetics and Genomics in Geneva (iGE3)
| | - Charna Dibner
- Department of Medical Specialties, Division of Endocrinology, Diabetes, Hypertension and Nutrition, Diabetes Center, University of Geneva Medical School, Institute of Genetics and Genomics in Geneva (iGE3);
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Redox and Metabolic Oscillations in the Clockwork. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-3-319-27069-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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A Period2 Phosphoswitch Regulates and Temperature Compensates Circadian Period. Mol Cell 2016; 60:77-88. [PMID: 26431025 DOI: 10.1016/j.molcel.2015.08.022] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 06/01/2015] [Accepted: 08/25/2015] [Indexed: 01/05/2023]
Abstract
Period (PER) protein phosphorylation is a critical regulator of circadian period, yet an integrated understanding of the role and interaction between phosphorylation sites that can both increase and decrease PER2 stability remains elusive. Here, we propose a phosphoswitch model, where two competing phosphorylation sites determine whether PER2 has a fast or slow degradation rate. This mathematical model accurately reproduces the three-stage degradation kinetics of endogenous PER2. We predict and demonstrate that the phosphoswitch is intrinsically temperature sensitive, slowing down PER2 degradation as a result of faster reactions at higher temperatures. The phosphoswitch provides a biochemical mechanism for circadian temperature compensation of circadian period. This phosphoswitch additionally explains the phenotype of Familial Advanced Sleep Phase (FASP) and CK1ε(tau) genetic circadian rhythm disorders, metabolic control of PER2 stability, and how drugs that inhibit CK1 alter period. The phosphoswitch provides a general mechanism to integrate diverse stimuli to regulate circadian period.
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Benegiamo G, Brown SA, Panda S. RNA Dynamics in the Control of Circadian Rhythm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:107-22. [PMID: 27256384 DOI: 10.1007/978-3-319-29073-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The circadian oscillator is based on transcription-translation feedback loops that generate 24 h oscillations in gene expression. Although circadian regulation of mRNA expression at the transcriptional level is one of the most important steps for the generation of circadian rhythms within the cell, multiple lines of evidence point to a disconnect between transcript oscillation and protein oscillation. This can be explained by regulatory RNA-binding proteins acting on the nascent transcripts to modulate their processing, export, translation and degradation rates. In this chapter we will review what is known about the different steps involved in circadian gene expression from transcription initiation to mRNA stability and translation efficiency. The role of ribonucleoprotein particles in the generation of rhythmic gene expression is only starting to be elucidated, but it is likely that they cooperate with the basal transcriptional machinery to help to maintain the precision of the clock under diverse cellular and environmental conditions.
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Affiliation(s)
- Giorgia Benegiamo
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Satchidananda Panda
- Salk Institute for Biological Studies, 10010, North Torrey Pines Road, La Jolla, CA, 92037, USA.
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Hatakeyama TS, Kaneko K. Reciprocity Between Robustness of Period and Plasticity of Phase in Biological Clocks. PHYSICAL REVIEW LETTERS 2015; 115:218101. [PMID: 26636874 DOI: 10.1103/physrevlett.115.218101] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 06/05/2023]
Abstract
Circadian clocks exhibit the robustness of period and plasticity of phase against environmental changes such as temperature and nutrient conditions. Thus far, however, it is unclear how both are simultaneously achieved. By investigating distinct models of circadian clocks, we demonstrate reciprocity between robustness and plasticity: higher robustness in the period implies higher plasticity in the phase, where changes in period and in phase follow a linear relationship with a negative coefficient. The robustness of period is achieved by the adaptation on the limit cycle via a concentration change of a buffer molecule, whose temporal change leads to a phase shift following a shift of the limit-cycle orbit in phase space. Generality of reciprocity in clocks with the adaptation mechanism is confirmed with theoretical analysis of simple models, while biological significance is discussed.
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Affiliation(s)
- Tetsuhiro S Hatakeyama
- Department of Basic Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kunihiko Kaneko
- Department of Basic Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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Temperature compensation and temperature sensation in the circadian clock. Proc Natl Acad Sci U S A 2015; 112:E6284-92. [PMID: 26578788 DOI: 10.1073/pnas.1511215112] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
All known circadian clocks have an endogenous period that is remarkably insensitive to temperature, a property known as temperature compensation, while at the same time being readily entrained by a diurnal temperature oscillation. Although temperature compensation and entrainment are defining features of circadian clocks, their mechanisms remain poorly understood. Most models presume that multiple steps in the circadian cycle are temperature-dependent, thus facilitating temperature entrainment, but then insist that the effect of changes around the cycle sums to zero to enforce temperature compensation. An alternative theory proposes that the circadian oscillator evolved from an adaptive temperature sensor: a gene circuit that responds only to temperature changes. This theory implies that temperature changes should linearly rescale the amplitudes of clock component oscillations but leave phase relationships and shapes unchanged. We show using timeless luciferase reporter measurements and Western blots against TIMELESS protein that this prediction is satisfied by the Drosophila circadian clock. We also review evidence for pathways that couple temperature to the circadian clock, and show previously unidentified evidence for coupling between the Drosophila clock and the heat-shock pathway.
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Perrin L, Loizides-Mangold U, Skarupelova S, Pulimeno P, Chanon S, Robert M, Bouzakri K, Modoux C, Roux-Lombard P, Vidal H, Lefai E, Dibner C. Human skeletal myotubes display a cell-autonomous circadian clock implicated in basal myokine secretion. Mol Metab 2015; 4:834-45. [PMID: 26629407 PMCID: PMC4632112 DOI: 10.1016/j.molmet.2015.07.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 07/27/2015] [Accepted: 07/30/2015] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE Circadian clocks are functional in all light-sensitive organisms, allowing an adaptation to the external world in anticipation of daily environmental changes. In view of the potential role of the skeletal muscle clock in the regulation of glucose metabolism, we aimed to characterize circadian rhythms in primary human skeletal myotubes and investigate their roles in myokine secretion. METHODS We established a system for long-term bioluminescence recording in differentiated human myotubes, employing lentivector gene delivery of the Bmal1-luciferase and Per2-luciferase core clock reporters. Furthermore, we disrupted the circadian clock in skeletal muscle cells by transfecting siRNA targeting CLOCK. Next, we assessed the basal secretion of a large panel of myokines in a circadian manner in the presence or absence of a functional clock. RESULTS Bioluminescence reporter assays revealed that human skeletal myotubes, synchronized in vitro, exhibit a self-sustained circadian rhythm, which was further confirmed by endogenous core clock transcript expression. Moreover, we demonstrate that the basal secretion of IL-6, IL-8 and MCP-1 by synchronized skeletal myotubes has a circadian profile. Importantly, the secretion of IL-6 and several additional myokines was strongly downregulated upon siClock-mediated clock disruption. CONCLUSIONS Our study provides for the first time evidence that primary human skeletal myotubes possess a high-amplitude cell-autonomous circadian clock, which could be attenuated. Furthermore, this oscillator plays an important role in the regulation of basal myokine secretion by skeletal myotubes.
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Affiliation(s)
- Laurent Perrin
- Division of Endocrinology, Diabetes and Nutrition, Department of Clinical Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ursula Loizides-Mangold
- Division of Endocrinology, Diabetes and Nutrition, Department of Clinical Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Svetlana Skarupelova
- Division of Endocrinology, Diabetes and Nutrition, Department of Clinical Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pamela Pulimeno
- Division of Endocrinology, Diabetes and Nutrition, Department of Clinical Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Stephanie Chanon
- CarMeN Laboratory, INSERM U1060, INRA 1397, University Lyon 1, Oullins, France
| | - Maud Robert
- Department of Digestive and Bariatric Surgery, Edouard Herriot Hospital, Lyon, France
| | - Karim Bouzakri
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christine Modoux
- Division of Immunology and Allergy, Department of Medical Specialties, University Hospital and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pascale Roux-Lombard
- Division of Immunology and Allergy, Department of Medical Specialties, University Hospital and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Hubert Vidal
- CarMeN Laboratory, INSERM U1060, INRA 1397, University Lyon 1, Oullins, France
| | - Etienne Lefai
- CarMeN Laboratory, INSERM U1060, INRA 1397, University Lyon 1, Oullins, France
| | - Charna Dibner
- Division of Endocrinology, Diabetes and Nutrition, Department of Clinical Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Goda K, Hatta‐Ohashi Y, Akiyoshi R, Sugiyama T, Sakai I, Takahashi T, Suzuki H. Combining fluorescence and bioluminescence microscopy. Microsc Res Tech 2015; 78:715-22. [PMID: 26096873 PMCID: PMC4745033 DOI: 10.1002/jemt.22529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/09/2015] [Indexed: 11/08/2022]
Abstract
Bioluminescence microscopy has revealed that gene expression in individual cells can respond differently to the same stimulus. To understand this phenomenon, it is important to sequentially observe the series of events from cellular signal transduction to gene expression regulated by specific transcription factors derived from signaling cascades in individual cells. However, these processes have been separately analyzed with fluorescence and bioluminescence microscopy. Furthermore, in culture medium, the background fluorescence of luciferin-a substrate of luciferase in promoter assays of gene expression in cultured cells-confounds the simultaneous observation of fluorescence and bioluminescence. Therefore, we optimized conditions for optical filter sets based on spectral properties and the luciferin concentration based on cell permeability for fluorescence observation combined with bioluminescence microscopy. An excitation and emission filter set (492-506 nm and 524-578 nm) was suitable for green fluorescent protein and yellow fluorescent protein imaging of cells, and >100 μM luciferin was acceptable in culture medium based on kinetic constants and the estimated intracellular concentration. Using these parameters, we present an example of sequential fluorescence and bioluminescence microscopic observation of signal transduction (translocation of protein kinase C alpha from the cytoplasm to the plasma membrane) coupled with activation of gene expression by nuclear factor of kappa light polypeptide B in individual cells and show that the gene expression response is not completely concordant with upstream signaling following stimulation with phorbol-12-myristate-13-acetate. Our technique is a powerful imaging tool for analysis of heterogeneous gene expression together with upstream signaling in live single cells.
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Affiliation(s)
- Kazuhito Goda
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
| | - Yoko Hatta‐Ohashi
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
| | - Ryutaro Akiyoshi
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
| | - Takashi Sugiyama
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
| | - Ikuko Sakai
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
| | - Takeo Takahashi
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
| | - Hirobumi Suzuki
- Corporate Research and Development Center, Olympus CorporationHachiojiTokyo192‐8512Japan
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Nakajima M, Koinuma S, Shigeyoshi Y. Reduction of translation rate stabilizes circadian rhythm and reduces the magnitude of phase shift. Biochem Biophys Res Commun 2015; 464:354-9. [PMID: 26141234 DOI: 10.1016/j.bbrc.2015.06.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
Abstract
In the intracellular environment, the circadian oscillator is exposed to molecular noise. Nevertheless, cellular rhythms are robust and show almost constant period length for several weeks. To find which molecular processes modulate the stability, we examined the effects of a sublethal dose of inhibitors for processes in the molecular clock. Inhibition of PER1/2 phosphorylation by CKIε/δ led to reduced amplitude and enhancement of damping, suggesting that inhibition of this process destabilized oscillation. In contrast, moderate inhibition of translation led to stabilization of the circadian oscillation. Moreover, inhibition of translation also reduced magnitude of phase shift. These results suggest that some specific molecular processes are crucial for stabilizing the circadian rhythm, and that the molecular clock may be stabilized by optimizing parameters of some crucial processes in the primary negative feedback loop. Moreover, our findings also suggested that rhythm stability is closely associated with phase stability against stimuli.
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Affiliation(s)
- Masato Nakajima
- Department of Anatomy and Neurobiology, Kinki University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan.
| | - Satoshi Koinuma
- Department of Anatomy and Neurobiology, Kinki University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kinki University Faculty of Medicine, 377-2 Ohno-Higashi, Osakasayama City, Osaka 589-8511, Japan.
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Tong X, Zhang D, Arthurs B, Li P, Durudogan L, Gupta N, Yin L. Palmitate Inhibits SIRT1-Dependent BMAL1/CLOCK Interaction and Disrupts Circadian Gene Oscillations in Hepatocytes. PLoS One 2015; 10:e0130047. [PMID: 26075729 PMCID: PMC4468094 DOI: 10.1371/journal.pone.0130047] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/15/2015] [Indexed: 12/12/2022] Open
Abstract
Elevated levels of serum saturated fatty acid palmitate have been shown to promote insulin resistance, increase cellular ROS production, and trigger cell apoptosis in hepatocytes during the development of obesity. However, it remains unclear whether palmitate directly impacts the circadian clock in hepatocytes, which coordinates nutritional inputs and hormonal signaling with downstream metabolic outputs. Here we presented evidence that the molecular clock is a novel target of palmitate in hepatocytes. Palmitate exposure at low dose inhibits the molecular clock activity and suppresses the cyclic expression of circadian targets including Dbp, Nr1d1 and Per2 in hepatocytes. Palmitate treatment does not seem to alter localization or reduce protein expression of BMAL1 and CLOCK, the two core components of the molecular clock in hepatocytes. Instead, palmitate destabilizes the protein-protein interaction between BMAL1-CLOCK in a dose and time-dependent manner. Furthermore, we showed that SIRT1 activators could reverse the inhibitory action of palmitate on BMAL1-CLOCK interaction and the clock gene expression, whereas inhibitors of NAD synthesis mimic the palmitate effects on the clock function. In summary, our findings demonstrated that palmitate inhibits the clock function by suppressing SIRT1 function in hepatocytes.
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Affiliation(s)
- Xin Tong
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Deqiang Zhang
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Blake Arthurs
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Pei Li
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Leigh Durudogan
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Neil Gupta
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Lei Yin
- Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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Abstract
Most living beings, including humans, must adapt to rhythmically occurring daily changes in their environment that are generated by the Earth's rotation. In the course of evolution, these organisms have acquired an internal circadian timing system that can anticipate environmental oscillations and thereby govern their rhythmic physiology in a proactive manner. In mammals, the circadian timing system coordinates virtually all physiological processes encompassing vigilance states, metabolism, endocrine functions and cardiovascular activity. Research performed during the past two decades has established that almost every cell in the body possesses its own circadian timekeeper. The resulting clock network is organized in a hierarchical manner. A master pacemaker, located in the suprachiasmatic nucleus (SCN) of the hypothalamus, is synchronized every day to the photoperiod. In turn, the SCN determines the phase of the cellular clocks in peripheral organs through a wide variety of signalling pathways dependent on feeding cycles, body temperature rhythms, oscillating bloodborne signals and, in some organs, inputs of the peripheral nervous system. A major purpose of circadian clocks in peripheral tissues is the temporal orchestration of key metabolic processes, including food processing (metabolism and xenobiotic detoxification). Here, we review some recent findings regarding the molecular and cellular composition of the circadian timing system and discuss its implications for the temporal coordination of metabolism in health and disease. We focus primarily on metabolic disorders such as obesity and type 2 diabetes, although circadian misalignments (shiftwork or 'social jet lag') have also been associated with the aetiology of human malignancies.
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Affiliation(s)
- C Dibner
- Department of Endocrinology, Diabetes, Nutrition and Hypertension, University Hospital of Geneva, Geneva, Switzerland
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Gnocchi D, Pedrelli M, Hurt-Camejo E, Parini P. Lipids around the Clock: Focus on Circadian Rhythms and Lipid Metabolism. BIOLOGY 2015; 4:104-32. [PMID: 25665169 PMCID: PMC4381220 DOI: 10.3390/biology4010104] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/28/2015] [Indexed: 12/24/2022]
Abstract
Disorders of lipid and lipoprotein metabolism and transport are responsible for the development of a large spectrum of pathologies, ranging from cardiovascular diseases, to metabolic syndrome, even to tumour development. Recently, a deeper knowledge of the molecular mechanisms that control our biological clock and circadian rhythms has been achieved. From these studies it has clearly emerged how the molecular clock tightly regulates every aspect of our lives, including our metabolism. This review analyses the organisation and functioning of the circadian clock and its relevance in the regulation of physiological processes. We also describe metabolism and transport of lipids and lipoproteins as an essential aspect for our health, and we will focus on how the circadian clock and lipid metabolism are greatly interconnected. Finally, we discuss how a deeper knowledge of this relationship might be useful to improve the recent spread of metabolic diseases.
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Affiliation(s)
- Davide Gnocchi
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, 14186, Sweden.
| | - Matteo Pedrelli
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, 14186, Sweden.
- Strategy and Externalization, CVMD iMED, AstraZeneca, R&D, Mölndal, SE-431 83, Sweden.
| | - Eva Hurt-Camejo
- Strategy and Externalization, CVMD iMED, AstraZeneca, R&D, Mölndal, SE-431 83, Sweden.
| | - Paolo Parini
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, Stockholm, 14186, Sweden.
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46
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Abstract
For a biological oscillator to function as a circadian pacemaker that confers a fitness advantage, its timing functions must be stable in response to environmental and metabolic fluctuations. One such stability enhancer, temperature compensation, has long been a defining characteristic of these timekeepers. However, an accurate biological timekeeper must also resist changes in metabolism, and this review suggests that temperature compensation is actually a subset of a larger phenomenon, namely metabolic compensation, which maintains the frequency of circadian oscillators in response to a host of factors that impinge on metabolism and would otherwise destabilize these clocks. The circadian system of prokaryotic cyanobacteria is an illustrative model because it is composed of transcriptional and nontranscriptional oscillators that are coupled to promote resilience. Moreover, the cyanobacterial circadian program regulates gene activity and metabolic pathways, and it can be manipulated to improve the expression of bioproducts that have practical value.
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47
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Nieto PS, Revelli JA, Garbarino-Pico E, Condat CA, Guido ME, Tamarit FA. Effects of different per translational kinetics on the dynamics of a core circadian clock model. PLoS One 2015; 10:e0115067. [PMID: 25607544 PMCID: PMC4301915 DOI: 10.1371/journal.pone.0115067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 11/18/2014] [Indexed: 11/19/2022] Open
Abstract
Living beings display self-sustained daily rhythms in multiple biological processes, which persist in the absence of external cues since they are generated by endogenous circadian clocks. The period (per) gene is a central player within the core molecular mechanism for keeping circadian time in most animals. Recently, the modulation PER translation has been reported, both in mammals and flies, suggesting that translational regulation of clock components is important for the proper clock gene expression and molecular clock performance. Because translational regulation ultimately implies changes in the kinetics of translation and, therefore, in the circadian clock dynamics, we sought to study how and to what extent the molecular clock dynamics is affected by the kinetics of PER translation. With this objective, we used a minimal mathematical model of the molecular circadian clock to qualitatively characterize the dynamical changes derived from kinetically different PER translational mechanisms. We found that the emergence of self-sustained oscillations with characteristic period, amplitude, and phase lag (time delays) between per mRNA and protein expression depends on the kinetic parameters related to PER translation. Interestingly, under certain conditions, a PER translation mechanism with saturable kinetics introduces longer time delays than a mechanism ruled by a first-order kinetics. In addition, the kinetic laws of PER translation significantly changed the sensitivity of our model to parameters related to the synthesis and degradation of per mRNA and PER degradation. Lastly, we found a set of parameters, with realistic values, for which our model reproduces some experimental results reported recently for Drosophila melanogaster and we present some predictions derived from our analysis.
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Affiliation(s)
- Paula S. Nieto
- Instituto de Física Enrique Gaviola (IFEG-CONICET) and Facultad de Matemática, Astronomía y Física (FaMAF), Universidad Nacional de Córdoba (UNC). Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - Jorge A. Revelli
- Instituto de Física Enrique Gaviola (IFEG-CONICET) and Facultad de Matemática, Astronomía y Física (FaMAF), Universidad Nacional de Córdoba (UNC). Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - Eduardo Garbarino-Pico
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET) and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC). Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - Carlos A. Condat
- Instituto de Física Enrique Gaviola (IFEG-CONICET) and Facultad de Matemática, Astronomía y Física (FaMAF), Universidad Nacional de Córdoba (UNC). Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - Mario E. Guido
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC-CONICET) and Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba (UNC). Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
| | - Francisco A. Tamarit
- Instituto de Física Enrique Gaviola (IFEG-CONICET) and Facultad de Matemática, Astronomía y Física (FaMAF), Universidad Nacional de Córdoba (UNC). Ciudad Universitaria, CP:X5000HUA Córdoba, Argentina
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48
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Abstract
Circadian clocks are present in most cells and are essential for maintenance of daily rhythms in physiology, mood, and cognition. Thus, not only neurons of the central circadian pacemaker but also many other peripheral tissues possess the same functional and self-sustained circadian clocks. Surprisingly, however, their properties vary widely within the human population. In recent years, this clock variance has been studied extensively both in health and in disease using robust lentivirus-based reporter technologies to probe circadian function in human peripheral cells as proxies for those in neurologically and physiologically relevant but inaccessible tissues. The same procedures can be used to investigate other conserved signal transduction cascades affecting multiple aspects of human physiology, behavior, and disease. Accessing gene expression variation within human populations via these powerful in vitro cell-based technologies could provide important insights into basic phenotypic diversity or to better interpret patterns of gene expression variation in disease.
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Affiliation(s)
- Ludmila Gaspar
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Steven A Brown
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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49
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Abstract
Three properties are most often attributed to the circadian clock: a ca. 24-h free-running rhythm, temperature compensation of the circadian rhythm, and its entrainment to zeitgeber cycles. Relatively few experiments, however, are performed under entrainment conditions. Rather, most chronobiology protocols concern constant conditions. We have turned this paradigm around and used entrainment to study the circadian clock in organisms where a free-running rhythm is weak or lacking. We describe two examples therein: Caenorhabditis elegans and Saccharomyces cerevisiae. By probing the system with zeitgeber cycles that have various structures and amplitudes, we can demonstrate the establishment of systematic entrained phase angles in these organisms. We conclude that entrainment can be utilized to discover hitherto unknown circadian clocks and we discuss the implications of using entrainment more broadly, even in model systems that show robust free-running rhythms.
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50
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Philippe J, Dibner C. Thyroid circadian timing: roles in physiology and thyroid malignancies. J Biol Rhythms 2014; 30:76-83. [PMID: 25411240 DOI: 10.1177/0748730414557634] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The circadian clock represents an anticipatory mechanism, well preserved in evolution. It has a critical impact on most aspects of the physiology of light-sensitive organisms. These rhythmic processes are governed by environmental cues (fluctuations in light intensity and temperature), an internal circadian timing system, and interactions between this timekeeping system and environmental signals. Endocrine body rhythms, including hypothalamic-pituitary-thyroid (HPT) axis rhythms, are tightly regulated by the circadian system. Although the circadian profiles of thyroid-releasing hormone (TRH), thyroid-stimulating hormone (TSH), thyroxine (T4), and triiodothyronine (T3) in blood have been well described, relatively few studies have analyzed molecular mechanisms governing the circadian regulation of HPT axis function. In this review, we will discuss the latest findings in the area of complex regulation of thyroid gland function by the circadian oscillator. We will also highlight the molecular makeup of the human thyroid oscillator as well as the potential link between thyroid malignant transformation and alterations in the clockwork.
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Affiliation(s)
- Jacques Philippe
- Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland Division of Endocrinology, Diabetes, Hypertension and Nutrition, University Hospital of Geneva, Geneva, Switzerland
| | - Charna Dibner
- Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland Division of Endocrinology, Diabetes, Hypertension and Nutrition, University Hospital of Geneva, Geneva, Switzerland
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