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Hajdu A, Nyári D, Terecskei K, Gyula P, Ádám É, Dobos O, Mérai Z, Kozma-Bognár L. LIP1 Regulates the Plant Circadian Oscillator by Modulating the Function of the Clock Component GIGANTEA. Cells 2024; 13:1503. [PMID: 39273073 PMCID: PMC11394198 DOI: 10.3390/cells13171503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/04/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
Circadian clocks are biochemical timers regulating many physiological and molecular processes according to the day/night cycles. The function of the oscillator relies on negative transcriptional/translational feedback loops operated by the so-called clock genes and the encoded clock proteins. Previously, we identified the small GTPase LIGHT INSENSITIVE PERIOD 1 (LIP1) as a circadian-clock-associated protein that regulates light input to the clock in the model plant Arabidopsis thaliana. We showed that LIP1 is also required for suppressing red and blue light-mediated photomorphogenesis, pavement cell shape determination and tolerance to salt stress. Here, we demonstrate that LIP1 is present in a complex of clock proteins GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB 1 (TOC1). LIP1 participates in this complex via GUANINE EX-CHANGE FACTOR 7. Analysis of genetic interactions proved that LIP1 affects the oscillator via modulating the function of GI. We show that LIP1 and GI independently and additively regulate photomorphogenesis and salt stress responses, whereas controlling cell shape and photoperiodic flowering are not shared functions of LIP1 and GI. Collectively, our results suggest that LIP1 affects a specific function of GI, possibly by altering binding of GI to downstream signalling components.
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Affiliation(s)
- Anita Hajdu
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - Dóra Nyári
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, H-6726 Szeged, Hungary
| | - Kata Terecskei
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
| | - Péter Gyula
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, H-2100 Gödöllő, Hungary
| | - Éva Ádám
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, H-6720 Szeged, Hungary
| | - Orsolya Dobos
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant Biology GmbH, 1030 Vienna, Austria
| | - László Kozma-Bognár
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, H-6726 Szeged, Hungary
- Institute of Plant Biology, HUN-REN Biological Research Centre, H-6726 Szeged, Hungary
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2
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Rajan PK, Udoh UAS, Finley R, Pierre SV, Sanabria J. The Biological Clock of Liver Metabolism in Metabolic Dysfunction-Associated Steatohepatitis Progression to Hepatocellular Carcinoma. Biomedicines 2024; 12:1961. [PMID: 39335475 PMCID: PMC11428469 DOI: 10.3390/biomedicines12091961] [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: 07/12/2024] [Revised: 08/12/2024] [Accepted: 08/19/2024] [Indexed: 09/30/2024] Open
Abstract
Circadian rhythms are endogenous behavioral or physiological cycles that are driven by a daily biological clock that persists in the absence of geophysical or environmental temporal cues. Circadian rhythm-related genes code for clock proteins that rise and fall in rhythmic patterns driving biochemical signals of biological processes from metabolism to physiology and behavior. Clock proteins have a pivotal role in liver metabolism and homeostasis, and their disturbances are implicated in various liver disease processes. Encoded genes play critical roles in the initiation and progression of metabolic dysfunction-associated steatohepatitis (MASH) to hepatocellular carcinoma (HCC) and their proteins may become diagnostic markers as well as therapeutic targets. Understanding molecular and metabolic mechanisms underlying circadian rhythms will aid in therapeutic interventions and may have broader clinical applications. The present review provides an overview of the role of the liver's circadian rhythm in metabolic processes in health and disease, emphasizing MASH progression and the oncogenic associations that lead to HCC.
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Affiliation(s)
- Pradeep Kumar Rajan
- Marshall Institute for Interdisciplinary Research, Huntington, WV 25703, USA
- Department of Surgery, School of Medicine, Marshall University, Huntington, WV 25701, USA
| | - Utibe-Abasi S Udoh
- Marshall Institute for Interdisciplinary Research, Huntington, WV 25703, USA
- Department of Surgery, School of Medicine, Marshall University, Huntington, WV 25701, USA
| | - Robert Finley
- Department of Surgery, School of Medicine, Marshall University, Huntington, WV 25701, USA
| | - Sandrine V Pierre
- Marshall Institute for Interdisciplinary Research, Huntington, WV 25703, USA
| | - Juan Sanabria
- Marshall Institute for Interdisciplinary Research, Huntington, WV 25703, USA
- Department of Surgery, School of Medicine, Marshall University, Huntington, WV 25701, USA
- Department of Nutrition and Metabolomic Core Facility, School of Medicine, Case Western Reserve University, Cleveland, OH 44100, USA
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3
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Xie X, Zhang M, Luo H. Regulation of metabolism by circadian rhythms: Support from time-restricted eating, intestinal microbiota & omics analysis. Life Sci 2024; 351:122814. [PMID: 38857654 DOI: 10.1016/j.lfs.2024.122814] [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: 02/18/2024] [Revised: 05/05/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Circadian oscillatory system plays a key role in coordinating the metabolism of most organisms. Perturbation of genetic effects and misalignment of circadian rhythms result in circadian dysfunction and signs of metabolic disorders. The eating-fasting cycle can act on the peripheral circadian clocks, bypassing the photoperiod. Therefore, time-restricted eating (TRE) can improve metabolic health by adjusting eating rhythms, a process achieved through reprogramming of circadian genomes and metabolic programs at different tissue levels or remodeling of the intestinal microbiota, with omics technology allowing visualization of the regulatory processes. Here, we review recent advances in circadian regulation of metabolism, focus on the potential application of TRE for rescuing circadian dysfunction and metabolic disorders with the contribution of intestinal microbiota in between, and summarize the significance of omics technology.
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Affiliation(s)
- Ximei Xie
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, PR China
| | - Mengjie Zhang
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, PR China
| | - Hailing Luo
- State Key Laboratory of Animal Nutrition and Feeding, College of Animal Science and Technology, China Agricultural University, PR China.
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4
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Otobe Y, Jeong EM, Ito S, Shinohara Y, Kurabayashi N, Aiba A, Fukada Y, Kim JK, Yoshitane H. Phosphorylation of DNA-binding domains of CLOCK-BMAL1 complex for PER-dependent inhibition in circadian clock of mammalian cells. Proc Natl Acad Sci U S A 2024; 121:e2316858121. [PMID: 38805270 PMCID: PMC11161756 DOI: 10.1073/pnas.2316858121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/03/2024] [Indexed: 05/30/2024] Open
Abstract
In mammals, CLOCK and BMAL1 proteins form a heterodimer that binds to E-box sequences and activates transcription of target genes, including Period (Per). Translated PER proteins then bind to the CLOCK-BMAL1 complex to inhibit its transcriptional activity. However, the molecular mechanism and the impact of this PER-dependent inhibition on the circadian clock oscillation remain elusive. We previously identified Ser38 and Ser42 in a DNA-binding domain of CLOCK as phosphorylation sites at the PER-dependent inhibition phase. In this study, knockout rescue experiments showed that nonphosphorylatable (Ala) mutations at these sites shortened circadian period, whereas their constitutive-phospho-mimetic (Asp) mutations completely abolished the circadian rhythms. Similarly, we found that nonphosphorylatable (Ala) and constitutive-phospho-mimetic (Glu) mutations at Ser78 in a DNA-binding domain of BMAL1 also shortened the circadian period and abolished the rhythms, respectively. The mathematical modeling predicted that these constitutive-phospho-mimetic mutations weaken the DNA binding of the CLOCK-BMAL1 complex and that the nonphosphorylatable mutations inhibit the PER-dependent displacement (reduction of DNA-binding ability) of the CLOCK-BMAL1 complex from DNA. Biochemical experiments supported the importance of these phosphorylation sites for displacement of the complex in the PER2-dependent inhibition. Our results provide direct evidence that phosphorylation of CLOCK-Ser38/Ser42 and BMAL1-Ser78 plays a crucial role in the PER-dependent inhibition and the determination of the circadian period.
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Affiliation(s)
- Yuta Otobe
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
- Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo156-8506, Japan
| | - Eui Min Jeong
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon34141, Republic of Korea
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Shunsuke Ito
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
- Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo156-8506, Japan
| | - Yuta Shinohara
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine and Graduate School of Medicine, Hokkaido University, Kita-Ku, Sapporo060-0815, Japan
| | - Nobuhiro Kurabayashi
- Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo156-8506, Japan
| | - Atsu Aiba
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
| | - Yoshitaka Fukada
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
- Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo156-8506, Japan
| | - Jae Kyoung Kim
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon34141, Republic of Korea
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon34141, Republic of Korea
| | - Hikari Yoshitane
- Department of Biological Sciences, School of Science, The University of Tokyo, Bunkyo-ku, Tokyo113-0033, Japan
- Circadian Clock Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo156-8506, Japan
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5
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Rodríguez Ferrante G, Leone MJ. Solar clock and school start time effects on adolescents' chronotype and sleep: A review of a gap in the literature. J Sleep Res 2024; 33:e13974. [PMID: 37370220 DOI: 10.1111/jsr.13974] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/11/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023]
Abstract
Circadian rhythms are entrained by external factors such as sunlight and social cues, but also depend on internal factors such as age. Adolescents exhibit late chronotypes, but worldwide school starts early in the morning leading to unhealthy sleep habits. Several studies reported that adolescents benefit from later school start times. However, the effect of later school start time on different outcomes varies between studies, and most previous literature only takes into consideration the social clock (i.e. local time of school starting time) but not the solar clock (e.g. the distance between school start time and sunrise). Thus, there is an important gap in the literature: when assessing the effect of a school start time on chronotype and sleep of adolescents at different locations and/or seasons, the solar clock might differ and, consistently, the obtained results. For example, the earliest school start time for adolescents has been suggested to be 08:30 hours, but this school start time might correspond to different solar times at different times of the year, longitudes and latitudes. Here, we describe the available literature comparing different school start times, considering important factors such as geographic position, nationality, and the local school start time and its distance to sunrise. Then, we described and contrasted the relative role of both social and solar clocks on the chronotype and sleep of adolescents. As a whole, we point and discuss a gap in literature, suggesting that both clocks are relevant when addressing the effect of school start time on adolescents' chronotype and sleep.
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Affiliation(s)
- Guadalupe Rodríguez Ferrante
- Laboratorio de Neurociencia, Universidad Torcuato Di Tella, CONICET, Buenos Aires, Argentina
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Buenos Aires, Argentina
| | - María Juliana Leone
- Laboratorio de Neurociencia, Universidad Torcuato Di Tella, CONICET, Buenos Aires, Argentina
- Área de Educación, Escuela de Gobierno, Universidad Torcuato Di Tella, Buenos Aires, Argentina
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Kiperman T, Ma K. Circadian Clock in Muscle Disease Etiology and Therapeutic Potential for Duchenne Muscular Dystrophy. Int J Mol Sci 2024; 25:4767. [PMID: 38731986 PMCID: PMC11083552 DOI: 10.3390/ijms25094767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Circadian clock and clock-controlled output pathways exert temporal control in diverse aspects of skeletal muscle physiology, including the maintenance of muscle mass, structure, function, and metabolism. They have emerged as significant players in understanding muscle disease etiology and potential therapeutic avenues, particularly in Duchenne muscular dystrophy (DMD). This review examines the intricate interplay between circadian rhythms and muscle physiology, highlighting how disruptions of circadian regulation may contribute to muscle pathophysiology and the specific mechanisms linking circadian clock dysregulation with DMD. Moreover, we discuss recent advancements in chronobiological research that have shed light on the circadian control of muscle function and its relevance to DMD. Understanding clock output pathways involved in muscle mass and function offers novel insights into the pathogenesis of DMD and unveils promising avenues for therapeutic interventions. We further explore potential chronotherapeutic strategies targeting the circadian clock to ameliorate muscle degeneration which may inform drug development efforts for muscular dystrophy.
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Affiliation(s)
| | - Ke Ma
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA;
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7
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Schneps CM, Dunleavy R, Crane BR. Dissecting the Interaction between Cryptochrome and Timeless Reveals Underpinnings of Light-Dependent Recognition. Biochemistry 2024:10.1021/acs.biochem.3c00630. [PMID: 38294880 PMCID: PMC11289166 DOI: 10.1021/acs.biochem.3c00630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Circadian rhythms are determined by cell-autonomous transcription-translation feedback loops that entrain to environmental stimuli. In the model circadian clock of Drosophila melanogaster, the clock is set by the light-induced degradation of the core oscillator protein timeless (TIM) by the principal light-sensor cryptochrome (CRY). The cryo-EM structure of CRY bound to TIM revealed that within the extensive CRY:TIM interface, the TIM N-terminus binds into the CRY FAD pocket, in which FAD and the associated phosphate-binding loop (PBL) undergo substantial rearrangement. The TIM N-terminus involved in CRY binding varies in isoforms that facilitate the adaptation of flies to different light environments. Herein, we demonstrate, through peptide binding assays and pulsed-dipolar electron spin resonance (ESR) spectroscopy, that the TIM N-terminal peptide alone exhibits light-dependent binding to CRY and that the affinity of the interaction depends on the initiating methionine residue. Extensions to the TIM N-terminus that mimic less light-sensitive variants have substantially reduced interactions with CRY. Substitutions of CRY residues that couple to the flavin rearrangement in the CRY:TIM complex have dramatic effects on CRY light activation. CRY residues Arg237 on α8, Asn253, and Gln254 on the PBL are critical for the release of the CRY autoinhibitory C-terminal tail (CTT) and subsequent TIM binding. These key light-responsive elements of CRY are well conserved throughout Type I cryptochromes of invertebrates but not by cryptochromes of chordates and plants, which likely utilize a distinct light-activation mechanism.
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Affiliation(s)
| | - Robert Dunleavy
- Cornell University, Department of Chemistry & Chemical Biology, Ithaca, NY 14853
| | - Brian R. Crane
- Cornell University, Department of Chemistry & Chemical Biology, Ithaca, NY 14853
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Chen S, Zhang W, Li X, Cao Z, Liu C. DNA polymerase beta connects tumorigenicity with the circadian clock in liver cancer through the epigenetic demethylation of Per1. Cell Death Dis 2024; 15:78. [PMID: 38245510 PMCID: PMC10799862 DOI: 10.1038/s41419-024-06462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/22/2024]
Abstract
The circadian-controlled DNA repair exhibits a strong diurnal rhythm. Disruption in circadian clock and DNA repair is closely linked with hepatocellular carcinoma (HCC) progression, but the mechanism remains unknown. Here, we show that polymerase beta (POLB), a critical enzyme in the DNA base excision repair pathway, is rhythmically expressed at the translational level in mouse livers. Hepatic POLB dysfunction dampens clock homeostasis, whereas retards HCC progression, by mediating the methylation of the 4th CpG island on the 5'UTR of clock gene Per1. Clinically, POLB is overexpressed in human HCC samples and positively associated with poor prognosis. Furthermore, the hepatic rhythmicity of POLB protein expression is orchestrated by Calreticulin (CALR). Our findings provide important insights into the molecular mechanism underlying the synergy between clock and food signals on the POLB-driven BER system and reveal new clock-dependent carcinogenetic effects of POLB. Therefore, chronobiological modulation of POLB may help to promote precise interventions for HCC.
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Affiliation(s)
- Siyu Chen
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Wenxiang Zhang
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Xiao Li
- Department of Pathology, First Affiliated Hospital with Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zhengyu Cao
- Jiangsu Provincial Key Laboratory for TCM Evaluation and Translational Development, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing, 211198, Jiangsu, China.
- Chongqing Innovation Institute of China Pharmaceutical University, Chongqing, 401135, China.
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9
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [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: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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de Barros Dantas LL, Eldridge BM, Dorling J, Dekeya R, Lynch DA, Dodd AN. Circadian regulation of metabolism across photosynthetic organisms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:650-668. [PMID: 37531328 PMCID: PMC10953457 DOI: 10.1111/tpj.16405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 08/04/2023]
Abstract
Circadian regulation produces a biological measure of time within cells. The daily cycle in the availability of light for photosynthesis causes dramatic changes in biochemical processes in photosynthetic organisms, with the circadian clock having crucial roles in adaptation to these fluctuating conditions. Correct alignment between the circadian clock and environmental day-night cycles maximizes plant productivity through its regulation of metabolism. Therefore, the processes that integrate circadian regulation with metabolism are key to understanding how the circadian clock contributes to plant productivity. This forms an important part of exploiting knowledge of circadian regulation to enhance sustainable crop production. Here, we examine the roles of circadian regulation in metabolic processes in source and sink organ structures of Arabidopsis. We also evaluate possible roles for circadian regulation in root exudation processes that deposit carbon into the soil, and the nature of the rhythmic interactions between plants and their associated microbial communities. Finally, we examine shared and differing aspects of the circadian regulation of metabolism between Arabidopsis and other model photosynthetic organisms, and between circadian control of metabolism in photosynthetic and non-photosynthetic organisms. This synthesis identifies a variety of future research topics, including a focus on metabolic processes that underlie biotic interactions within ecosystems.
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Affiliation(s)
| | - Bethany M. Eldridge
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Jack Dorling
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Richard Dekeya
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Deirdre A. Lynch
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
| | - Antony N. Dodd
- Department of Cell and Developmental BiologyJohn Innes Centre, Norwich Research ParkNorwichUK
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Liu Z, Zhang J, Li S, Wang H, Ren B, Li J, Bao Z, Liu J, Guo M, Yang G, Chen L. Circadian control of ConA-induced acute liver injury and inflammatory response via Bmal1 regulation of Junb. JHEP Rep 2023; 5:100856. [PMID: 37791375 PMCID: PMC10542646 DOI: 10.1016/j.jhepr.2023.100856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 10/05/2023] Open
Abstract
Background & Aims Circadian rhythms play significant roles in immune responses, and many inflammatory processes in liver diseases are associated with malfunctioning molecular clocks. However, the significance of the circadian clock in autoimmune hepatitis (AIH), which is characterised by immune-mediated hepatocyte destruction and extensive inflammatory cytokine production, remains unclear. Methods We tested the difference in susceptibility to the immune-mediated liver injury induced by concanavalin A (ConA) at various time points throughout a day in mice and analysed the effects of global, hepatocyte, or myeloid cell deletion of the core clock gene, Bmal1 (basic helix-loop-helix ARNT-like 1), on liver injury and inflammatory responses. Multiple molecular biology techniques and mice with macrophage-specific knockdown of Junb, a Bmal1 target gene, were used to investigate the involvement of Junb in the circadian control of ConA-induced hepatitis. Results The susceptibility to ConA-induced liver injury is highly dependent on the timing of ConA injection. The treatment at Zeitgeber time 0 (lights on) triggers the highest mortality as well as the severest liver injury and inflammatory responses. Further study revealed that this timing effect was driven by macrophage, but not hepatocyte, Bmal1. Mechanistically, Bmal1 controls the diurnal variation of ConA-induced hepatitis by directly regulating the circadian transcription of Junb and promoting M1 macrophage activation. Inhibition of Junb in macrophages blunts the administration time-dependent effect of ConA and attenuates liver injury. Moreover, we demonstrated that Junb promotes macrophage inflammation by regulating AKT and extracellular signal-regulated kinase (ERK) signalling pathways. Conclusions Our findings uncover a critical role of the Bmal1-Junb-AKT/ERK axis in the circadian control of ConA-induced hepatitis and provide new insights into the prevention and treatment of AIH. Impact and Implications This study unveils a critical role of the Bmal1-Junb-AKT/ERK axis in the circadian control of ConA-induced liver injury, providing new insights into the prevention and treatment of immune-mediated hepatitis, including autoimmune hepatitis (AIH). The findings have scientific implications as they enhance our understanding of the circadian regulation of immune responses in liver diseases. Furthermore, clinically, this research offers opportunities for optimising treatment strategies in immune-mediated hepatitis by considering the timing of therapeutic interventions.
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Affiliation(s)
- Zhaiyi Liu
- School of Bioengineering, Dalian University of Technology, Dalian, China
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiayang Zhang
- Wuhu Hospital and Health Science Center, East China Normal University, Shanghai, China
| | - Shuyao Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Hui Wang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Baoyin Ren
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Jiazhi Li
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Zhiyue Bao
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Jiaxin Liu
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Meina Guo
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Guangrui Yang
- School of Clinical Medicine, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Lihong Chen
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
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12
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Nakagawa S, Yamaguchi Y. Spontaneous recurrence of a summer-like diel rhythm in the body temperature of the Syrian hamster after hibernation. Proc Biol Sci 2023; 290:20230922. [PMID: 37848068 PMCID: PMC10581774 DOI: 10.1098/rspb.2023.0922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 09/15/2023] [Indexed: 10/19/2023] Open
Abstract
Mammalian hibernation is a survival strategy characterized by metabolic suppression and drastically lowering body temperature (Tb), used during harsh seasons with food shortages and cold. The Syrian hamster commences hibernation in response to a short photoperiod and cold but spontaneously concludes hibernation after several months without environmental cues. Little is known about the changes in diel rhythms during hibernation. Using long-term and high-resolution Tb data, we analysed the diel Tb rhythm time-course changes in Syrian hamsters raised under summer-like conditions (long photoperiod (LP) and warm; LP-warm) and transferred to winter-like conditions (short photoperiod (SP) and cold; SP-cold). The diel Tb rhythm was undetectable during the hibernation period (HIBP), reappearing after the HIBP. The phase of this returning rhythm reverted to the LP entrainment phase characteristics despite the ambient SP and then re-entrained to the ambient SP as if the hamsters were transferred from the LP-warm to SP-cold conditions. The diel Tb rhythm reverted from the SP- to LP-type in a hibernation-dependent manner. Under constant dark and cold conditions, the circadian Tb rhythm recovered without photic stimuli following the HIBP. These findings suggest that hibernation involves a program that anticipates the ambient photoperiod when animals emerge from hibernation.
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Affiliation(s)
- Satoshi Nakagawa
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0819, Japan
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - Yoshifumi Yamaguchi
- Graduate School of Environmental Sciences, Hokkaido University, Sapporo 060-0819, Japan
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
- Inamori Research Institute for Science, Kyoto 600-8411, Japan
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13
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Gršković P, Korać P. Circadian Gene Variants in Diseases. Genes (Basel) 2023; 14:1703. [PMID: 37761843 PMCID: PMC10531145 DOI: 10.3390/genes14091703] [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: 07/22/2023] [Revised: 08/19/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
The circadian rhythm is a self-sustaining 24 h cycle that regulates physiological processes within the body, including cycles of alertness and sleepiness. Cells have their own intrinsic clock, which consists of several proteins that regulate the circadian rhythm of each individual cell. The core of the molecular clock in human cells consists of four main circadian proteins that work in pairs. The CLOCK-BMAL1 heterodimer and the PER-CRY heterodimer each regulate the other pair's expression, forming a negative feedback loop. Several other proteins are involved in regulating the expression of the main circadian genes, and can therefore also influence the circadian rhythm of cells. This review focuses on the existing knowledge regarding circadian gene variants in both the main and secondary circadian genes, and their association with various diseases, such as tumors, metabolic diseases, cardiovascular diseases, and sleep disorders.
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Affiliation(s)
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10 000 Zagreb, Croatia;
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14
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Wang D, Chen J, Yuan Y, Yu L, Yang G, Chen W. CRISPR/Cas9-mediated knockout of period reveals its function in the circadian rhythms of the diamondback moth Plutella xylostella. INSECT SCIENCE 2023; 30:637-649. [PMID: 36377278 DOI: 10.1111/1744-7917.13139] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/11/2022] [Accepted: 10/20/2022] [Indexed: 06/15/2023]
Abstract
Circadian clocks control the rhythmicity of many behaviors and physiological features of insects. To study the circadian clock of the moth Plutella xylostella, we employed CRISPR/Cas9-mediated genome editing to investigate the effect of loss of the clock gene period on the circadian rhythms. P. xylostella harbors a single copy of period. Phylogenetic analysis showed that P. xylostella PERIOD is more homologous to mouse PERIOD than the PERIOD proteins from bees, flies, mosquitos, and many other Lepidoptera, such as Danaus plexippus and Bombyx mori. The circadian rhythms in adult locomotor activity were altered in the period knockout strain of P. xylostella under light-dark (LD) and continuous dark (DD) conditions. Under the LD cycle, the wild-type moths displayed nocturnal activity with activity peaking very early after lights off and quickly declining after lights on. In contrast, the period knockout strain had no peak in activity when the lights were turned off and exhibited steady activity throughout the hours of darkness. Interestingly, under DD conditions, our results showed that the locomotor rhythm can be maintained without period gene, but at a lower rhythmicity ratio than wild-type. In addition, knockout of period in P. xylostella changed circadian rhythms patterns related to pupal eclosion, mating, egg-laying, and egg hatching. Mechanistically, loss of PERIOD disrupted the molecular rhythm of period and changed the clock transcription rhythm in the heads of the moths under LD and DD conditions. Together, our study indicates that the PERIOD is required for normal expression of many behavioral rhythms in P. xylostella.
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Affiliation(s)
- Danfeng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jing Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yao Yuan
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Lingqi Yu
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Control of Insect Pests, (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenfeng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, China
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15
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Lee K, Lee C. Generation of CRISPR-Cas9-mediated knockin mutant models in mice and MEFs for studies of polymorphism in clock genes. Sci Rep 2023; 13:8109. [PMID: 37208532 DOI: 10.1038/s41598-023-35203-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/14/2023] [Indexed: 05/21/2023] Open
Abstract
The creation of mutant mice has been invaluable for advancing biomedical science, but is too time- and resource-intensive for investigating the full range of mutations and polymorphisms. Cell culture models are therefore an invaluable complement to mouse models, especially for cell-autonomous pathways like the circadian clock. In this study, we quantitatively assessed the use of CRISPR to create cell models in mouse embryonic fibroblasts (MEFs) as compared to mouse models. We generated two point mutations in the clock genes Per1 and Per2 in mice and in MEFs using the same sgRNAs and repair templates for HDR and quantified the frequency of the mutations by digital PCR. The frequency was about an order of magnitude higher in mouse zygotes compared to that in MEFs. However, the mutation frequency in MEFs was still high enough for clonal isolation by simple screening of a few dozen individual cells. The Per mutant cells that we generated provide important new insights into the role of the PAS domain in regulating PER phosphorylation, a key aspect of the circadian clock mechanism. Quantification of the mutation frequency in bulk MEF populations provides a valuable basis for optimizing CRISPR protocols and time/resource planning for generating cell models for further studies.
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Affiliation(s)
- Kwangjun Lee
- Program in Neuroscience, Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA
| | - Choogon Lee
- Program in Neuroscience, Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL, 32306, USA.
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16
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Xu H, Wang X, Wei J, Zuo Y, Wang L. The Regulatory Networks of the Circadian Clock Involved in Plant Adaptation and Crop Yield. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091897. [PMID: 37176955 PMCID: PMC10181312 DOI: 10.3390/plants12091897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
Global climatic change increasingly threatens plant adaptation and crop yields. By synchronizing internal biological processes, including photosynthesis, metabolism, and responses to biotic and abiotic stress, with external environmental cures, such as light and temperature, the circadian clock benefits plant adaptation and crop yield. In this review, we focus on the multiple levels of interaction between the plant circadian clock and environmental factors, and we summarize recent progresses on how the circadian clock affects yield. In addition, we propose potential strategies for better utilizing the current knowledge of circadian biology in crop production in the future.
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Affiliation(s)
- Hang Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Wei
- College of Life Sciences, Changchun Normal University, Changchun 130032, China
| | - Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Liu X, Cai L, Zhu L, Tian Z, Shen Z, Cheng J, Zhang S, Li Z, Liu X. Mutation of the clock gene timeless disturbs diapause induction and adult emergence rhythm in Helicoverpa armigera. PEST MANAGEMENT SCIENCE 2023; 79:1876-1884. [PMID: 36654480 DOI: 10.1002/ps.7363] [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: 05/01/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Circadian rhythms are physical and behavioral changes that follow the 24-h cycle of Earth's light and temperature and are regulated by clock genes. Timeless (Tim) has been identified as a canonical clock gene in some insects, however, its functions have been little studied in lepidopteran pests. RESULTS To investigate Tim (HaTim) gene function in Helicoverpa armigera, an important lepidopteran pest, we obtained the HaTim mutant using the CRISPR/Cas9 gene editing system. Our results showed that the transcript levels of HaTim rhythmically peaked at night in heads of the wild larvae and adult, and the diel expression of HaTim was sensitive to photoperiod and temperature. The expression rhythms of other clock genes, such as HaPer, HaCry1, HaCry2 and HaCwo, were disturbed in the HaTim mutant larvae, as that stage is a sensitivity period for diapause induction. Fifth-instar wild-type larvae could be induced to pupate in diapause under a short-day photoperiod and low temperature, however, fifth-instar HaTim mutant larvae could not be induced under the same conditions. In addition, the emergence of wild-type adults peaked early at night, but the rhythm was disturbed in the HaTim mutant with arrhythmic expression of some clock genes, such as HaPer, HaCry1 and HaCwo in adults. CONCLUSION Our results suggest that the clock gene Tim is involved in diapause induction and adult emergence in H. armigera, and is a potential target gene for controlling pest. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiaoming Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Limei Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Lin Zhu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhiqiang Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhongjian Shen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jie Cheng
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Songdou Zhang
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhen Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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18
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Furtado A, Costa D, Lemos MC, Cavaco JE, Santos CRA, Quintela T. The impact of biological clock and sex hormones on the risk of disease. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 137:39-81. [PMID: 37709381 DOI: 10.1016/bs.apcsb.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Molecular clocks are responsible for defining 24-h cycles of behaviour and physiology that are called circadian rhythms. Several structures and tissues are responsible for generating these circadian rhythms and are named circadian clocks. The suprachiasmatic nucleus of the hypothalamus is believed to be the master circadian clock receiving light input via the optic nerve and aligning internal rhythms with environmental cues. Studies using both in vivo and in vitro methodologies have reported the relationship between the molecular clock and sex hormones. The circadian system is directly responsible for controlling the synthesis of sex hormones and this synthesis varies according to the time of day and phase of the estrous cycle. Sex hormones also directly interact with the circadian system to regulate circadian gene expression, adjust biological processes, and even adjust their own synthesis. Several diseases have been linked with alterations in either the sex hormone background or the molecular clock. So, in this chapter we aim to summarize the current understanding of the relationship between the circadian system and sex hormones and their combined role in the onset of several related diseases.
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Affiliation(s)
- André Furtado
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Portugal
| | - Diana Costa
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Portugal
| | - Manuel C Lemos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Portugal
| | - J Eduardo Cavaco
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Portugal
| | - Cecília R A Santos
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Portugal
| | - Telma Quintela
- CICS-UBI, Health Sciences Research Centre, University of Beira Interior, Portugal; UDI-IPG, Unidade de Investigação para o Desenvolvimento do Interior, Instituto Politécnico da Guarda, Guarda, Portugal.
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19
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Coskun A, Zarepour A, Zarrabi A. Physiological Rhythms and Biological Variation of Biomolecules: The Road to Personalized Laboratory Medicine. Int J Mol Sci 2023; 24:ijms24076275. [PMID: 37047252 PMCID: PMC10094461 DOI: 10.3390/ijms24076275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
The concentration of biomolecules in living systems shows numerous systematic and random variations. Systematic variations can be classified based on the frequency of variations as ultradian (<24 h), circadian (approximately 24 h), and infradian (>24 h), which are partly predictable. Random biological variations are known as between-subject biological variations that are the variations among the set points of an analyte from different individuals and within-subject biological variation, which is the variation of the analyte around individuals’ set points. The random biological variation cannot be predicted but can be estimated using appropriate measurement and statistical procedures. Physiological rhythms and random biological variation of the analytes could be considered the essential elements of predictive, preventive, and particularly personalized laboratory medicine. This systematic review aims to summarize research that have been done about the types of physiological rhythms, biological variations, and their effects on laboratory tests. We have searched the PubMed and Web of Science databases for biological variation and physiological rhythm articles in English without time restrictions with the terms “Biological variation, Within-subject biological variation, Between-subject biological variation, Physiological rhythms, Ultradian rhythms, Circadian rhythm, Infradian rhythms”. It was concluded that, for effective management of predicting, preventing, and personalizing medicine, which is based on the safe and valid interpretation of patients’ laboratory test results, both physiological rhythms and biological variation of the measurands should be considered simultaneously.
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20
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Kim K, Shin J, Kang TA, Kim B, Kim WC. CRISPR/Cas9-mediated AtGATA25 mutant represents a novel model for regulating hypocotyl elongation in Arabidopsis thaliana. Mol Biol Rep 2023; 50:31-41. [PMID: 36301462 PMCID: PMC9884261 DOI: 10.1007/s11033-022-07926-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/06/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Plants have evolved to adapt to the ever-changing environments through various morphological changes. An organism anticipates and responds to changes in its environment via the circadian clock, an endogenous oscillator lasting approximately 24 h. The circadian clock regulates various physiological processes, such as hypocotyl elongation in Arabidopsis thaliana. Phytochrome interacting factor 4 (PIF4), a member of the bHLH protein family, plays a vital hub role in light signaling pathways and temperature-mediated growth response mechanisms. PIF4 is controlled by the circadian clock and interacts with several factors. However, the components that regulate PIF4 transcription and activity are not clearly understood. METHODS AND RESULTS Here, we showed that the Arabidopsis thaliana GATA25 (AtGATA25) transcription factor plays a fundamental role in promoting hypocotyl elongation by positively regulating the expression of PIF4. This was confirmed to in the loss-of-function mutant of AtGATA25 via CRISPR/Cas9-mediated gene editing, which inhibits hypocotyl elongation and decreases the expression of PIF4. In contrast, the overexpression of AtGATA25 in transgenic plants resulted in increased expression of PIF4 and enhanced hypocotyl elongation. To better understand AtGATA25-mediated PIF4 transcriptional regulation, we analyzed the promoter region of the target gene PIF4 and characterized the role of GATA25 through transcriptional activation analysis. CONCLUSION Our findings suggest a novel role of the AtGATA25 transcription factor in hypocotyl elongation.
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Affiliation(s)
- Kihwan Kim
- Department of Applied Biosciences, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Juhyung Shin
- Department of Integrative Biology, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Tae-An Kang
- Department of Applied Biosciences, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Byeonggyu Kim
- Department of Integrative Biology, Kyungpook National University, 41566 Daegu, Republic of Korea
| | - Won-Chan Kim
- Department of Applied Biosciences, Kyungpook National University, 41566 Daegu, Republic of Korea ,Department of Integrative Biology, Kyungpook National University, 41566 Daegu, Republic of Korea
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21
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Patnaik A, Alavilli H, Rath J, Panigrahi KCS, Panigrahy M. Variations in Circadian Clock Organization & Function: A Journey from Ancient to Recent. PLANTA 2022; 256:91. [PMID: 36173529 DOI: 10.1007/s00425-022-04002-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Circadian clock components exhibit structural variations in different plant systems, and functional variations during various abiotic stresses. These variations bear relevance for plant fitness and could be important evolutionarily. All organisms on earth have the innate ability to measure time as diurnal rhythms that occur due to the earth's rotations in a 24-h cycle. Circadian oscillations arising from the circadian clock abide by its fundamental properties of periodicity, entrainment, temperature compensation, and oscillator mechanism, which is central to its function. Despite the fact that a myriad of research in Arabidopsis thaliana illuminated many detailed aspects of the circadian clock, many more variations in clock components' organizations and functions remain to get deciphered. These variations are crucial for sustainability and adaptation in different plant systems in the varied environmental conditions in which they grow. Together with these variations, circadian clock functions differ drastically even during various abiotic and biotic stress conditions. The present review discusses variations in the organization of clock components and their role in different plant systems and abiotic stresses. We briefly introduce the clock components, entrainment, and rhythmicity, followed by the variants of the circadian clock in different plant types, starting from lower non-flowering plants, marine plants, dicots to the monocot crop plants. Furthermore, we discuss the interaction of the circadian clock with components of various abiotic stress pathways, such as temperature, light, water stress, salinity, and nutrient deficiency with implications for the reprogramming during these stresses. We also update on recent advances in clock regulations due to post-transcriptional, post-translation, non-coding, and micro-RNAs. Finally, we end this review by summarizing the points of applicability, a remark on the future perspectives, and the experiments that could clear major enigmas in this area of research.
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Affiliation(s)
- Alena Patnaik
- School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha, 752050, India
| | - Hemasundar Alavilli
- Department of Bioresources Engineering, Sejong University, Seoul, 05006, South Korea
| | - Jnanendra Rath
- Institute of Science, Visva-Bharati Central University, Santiniketan, West Bengal, 731235, India
| | - Kishore C S Panigrahi
- School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha, 752050, India
| | - Madhusmita Panigrahy
- School of Biological Sciences, National Institute of Science Education and Research, Jatni, Odisha, 752050, India.
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22
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Morphofunctional State and Circadian Rhythms of the Liver of Female Rats under the Influence of Chronic Alcohol Intoxication and Constant Lighting. Int J Mol Sci 2022; 23:ijms231810744. [PMID: 36142658 PMCID: PMC9502101 DOI: 10.3390/ijms231810744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
A separate and combined effect of constant illumination and chronic alcohol intoxication (CAI) on diurnal dynamics of micromorphometric parameters of hepatocytes in female Wistar rats and p53, Ki-67, PER2, BMAL1, and ADH5 expression in these cells were studied. The increase in apoptotic activity and proliferation in all animals under the action of chronodestructors is shown. All experimental animals showed a decrease in BMAL1 expression and increase in PER2 expression; ADH5 is overexpressed under the influence of ethanol. Circadian rhythms (CRs) of BMAL1, PER2, p53, and Ki-67 expression persist in all groups, except combined action of chronodestructors, and ADH5 CRs persist in all groups—thus, these rhythms in females are quite stable. CRs of the hepatocyte nuclei area are preserved in all the studied groups, although they undergo a significant shift. At the same time, the CRs of the hepatocyte area are destroyed under the action of light, both independently and in combination with CAI, and the CR of the nuclear-cytoplasmic ratio (NCR) is destroyed by exposure to CAI. It can be assumed that CRs of the hepatocyte area are significantly affected by dark deprivation and NCR rhythm is sensitive to ethanol consumption, while the stability of studied genes’ expression rhythms at separate influences of studied chronodestructors is maintained by yet unknown adaptation mechanisms. It is necessary to note that, according to our previous studies of male rats, rat females show significantly greater stability of the studied CRs.
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23
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Buel SM, Debopadhaya S, De los Santos H, Edwards KM, David AM, Dao UH, Bennett KP, Hurley JM. The PAICE suite reveals circadian posttranscriptional timing of noncoding RNAs and spliceosome components in Mus musculus macrophages. G3 (BETHESDA, MD.) 2022; 12:6649694. [PMID: 35876788 PMCID: PMC9434326 DOI: 10.1093/g3journal/jkac176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/27/2022] [Indexed: 01/07/2023]
Abstract
Circadian rhythms broadly regulate physiological functions by tuning oscillations in the levels of mRNAs and proteins to the 24-h day/night cycle. Globally assessing which mRNAs and proteins are timed by the clock necessitates accurate recognition of oscillations in RNA and protein data, particularly in large omics data sets. Tools that employ fixed-amplitude models have previously been used to positive effect. However, the recognition of amplitude change in circadian oscillations required a new generation of analytical software to enhance the identification of these oscillations. To address this gap, we created the Pipeline for Amplitude Integration of Circadian Exploration suite. Here, we demonstrate the Pipeline for Amplitude Integration of Circadian Exploration suite's increased utility to detect circadian trends through the joint modeling of the Mus musculus macrophage transcriptome and proteome. Our enhanced detection confirmed extensive circadian posttranscriptional regulation in macrophages but highlighted that some of the reported discrepancy between mRNA and protein oscillations was due to noise in data. We further applied the Pipeline for Amplitude Integration of Circadian Exploration suite to investigate the circadian timing of noncoding RNAs, documenting extensive circadian timing of long noncoding RNAs and small nuclear RNAs, which control the recognition of mRNA in the spliceosome complex. By tracking oscillating spliceosome complex proteins using the PAICE suite, we noted that the clock broadly regulates the spliceosome, particularly the major spliceosome complex. As most of the above-noted rhythms had damped amplitude changes in their oscillations, this work highlights the importance of the PAICE suite in the thorough enumeration of oscillations in omics-scale datasets.
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Affiliation(s)
| | | | | | - Kaelyn M Edwards
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Alexandra M David
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Uyen H Dao
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kristin P Bennett
- Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180, USA,Institute for Data Exploration and Applications, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Jennifer M Hurley
- Corresponding author: Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Li W, Cheng Y, Zhang Y, Qian Y, Wu M, Huang W, Yang N, Liu Y. Shumian Capsule Improves the Sleep Disorder and Mental Symptoms Through Melatonin Receptors in Sleep-Deprived Mice. Front Pharmacol 2022; 13:925828. [PMID: 35873551 PMCID: PMC9304889 DOI: 10.3389/fphar.2022.925828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Healthy sleep is vital to maintaining the body's homeostasis. With the development of modern society, sleep disorder has gradually become one of the most epidemic health problems worldwide. Shumian capsule (SMC), a kind of traditional Chinese medicine (TCM) commonly used for insomnia, exhibits antidepressant and sedative effects in clinical practice. However, the underlying mechanisms have not been fully clarified. With the aid of a network pharmacology approach and function enrichment analysis, we identified the involvement of melatonin receptors in the antidepressant and sedative effects of SMC. In sleep-deprived mice, SMC treatment significantly alleviated insomnia and relevant mental alterations by improving both sleep latency and sleep duration. However, ramelteon, a selective melatonin receptor agonist that has been approved for the treatment of insomnia, only improved sleep latency. Additionally, SMC exhibited comparable effects on mental alterations with ramelteon as determined by an open-field test (OFT) and forced swimming test (FST). Mechanistically, we revealed that the melatonin receptor MT1 and MT2 signaling pathways involved the therapeutic effects of SMC. In addition to the single effect of traditional melatonin receptor agonists on treating sleep onset insomnia, SMC had therapeutic potential for various sleep disorders, such as sleep onset insomnia and sleep maintenance insomnia. Convergingly, our findings provide theoretical support for the clinical application of SMC.
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Affiliation(s)
- Wenhua Li
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yinlong Cheng
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yi Zhang
- Medical College, Tibet University, Lhasa, China
| | - Yazhi Qian
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Mo Wu
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wei Huang
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Nan Yang
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- *Correspondence: Nan Yang, ; Yanyong Liu,
| | - Yanyong Liu
- Department of Pharmacology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, China
- Medical College, Tibet University, Lhasa, China
- *Correspondence: Nan Yang, ; Yanyong Liu,
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25
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Mazzoccoli G. Chronobiology Meets Quantum Biology: A New Paradigm Overlooking the Horizon? Front Physiol 2022; 13:892582. [PMID: 35874510 PMCID: PMC9296773 DOI: 10.3389/fphys.2022.892582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/27/2022] [Indexed: 11/13/2022] Open
Abstract
Biological processes and physiological functions in living beings are featured by oscillations with a period of about 24 h (circadian) or cycle at the second and third harmonic (ultradian) of the basic frequency, driven by the biological clock. This molecular mechanism, common to all kingdoms of life, comprising animals, plants, fungi, bacteria, and protists, represents an undoubted adaptive advantage allowing anticipation of predictable changes in the environmental niche or of the interior milieu. Biological rhythms are the field of study of Chronobiology. In the last decade, growing evidence hints that molecular platforms holding up non-trivial quantum phenomena, including entanglement, coherence, superposition and tunnelling, bona fide evolved in biosystems. Quantum effects have been mainly implicated in processes related to electromagnetic radiation in the spectrum of visible light and ultraviolet rays, such as photosynthesis, photoreception, magnetoreception, DNA mutation, and not light related such as mitochondrial respiration and enzymatic activity. Quantum effects in biological systems are the field of study of Quantum Biology. Rhythmic changes at the level of gene expression, as well as protein quantity and subcellular distribution, confer temporal features to the molecular platform hosting electrochemical processes and non-trivial quantum phenomena. Precisely, a huge amount of molecules plying scaffold to quantum effects show rhythmic level fluctuations and this biophysical model implies that timescales of biomolecular dynamics could impinge on quantum mechanics biofunctional role. The study of quantum phenomena in biological cycles proposes a profitable “entanglement” between the areas of interest of these seemingly distant scientific disciplines to enlighten functional roles for quantum effects in rhythmic biosystems.
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26
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Lee JY, Jung E, Yeo H, Ahn SS, Lim Y, Lee YH. The Natural Janus Kinase Inhibitor Agerarin Downregulates Interleukin-4-Induced PER2 Expression in HaCaT Keratinocytes. Molecules 2022; 27:molecules27134205. [PMID: 35807451 PMCID: PMC9268509 DOI: 10.3390/molecules27134205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/16/2022] Open
Abstract
The circadian clock system is closely associated with inflammatory responses. Dysregulation of the circadian clock genes in the skin impairs the skin barrier function and affects the pathophysiology of atopic dermatitis. Interleukin 4 (IL-4) is a proinflammatory cytokine derived from T-helper type 2 cells; it plays a critical role in the pathogenesis of atopic dermatitis. Agerarin (6,7-dimethoxy-2,2-dimethyl-2H-chromene) is a natural JAK1/2/3 inhibitor isolated from Ageratum houstonianum that has a protective effect on the epidermal skin barrier. However, it remains unclear whether agerarin affects the circadian clock system. The aim of this study is to investigate the effect of agerarin on IL-4-induced PER2 gene expression in human keratinocytes through reverse transcription (RT)-PCR, quantitative real-time PCR (qPCR), immunoblotting, immunofluorescence microscopic analysis, and real-time bioluminescence analysis. We found that agerarin reduced IL-4-induced PER2 mRNA expression by suppressing the JAK-STAT3 pathway. In addition, real-time bioluminescence analysis in PER2:luc2p promoter-reporter cells revealed that agerarin restored the oscillatory rhythmicity of PER2 promoter activity altered by IL-4. These findings suggest that agerarin may be useful as a cosmeceutical agent against inflammatory skin conditions associated with disrupted circadian rhythms, such as atopic dermatitis.
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Affiliation(s)
- Jeong Yeon Lee
- Department of Biological Sciences, Sanghuh College of Lifesciences, Konkuk University, Seoul 05029, Korea; (J.Y.L.); (E.J.); (H.Y.); (S.S.A.)
| | - Euitaek Jung
- Department of Biological Sciences, Sanghuh College of Lifesciences, Konkuk University, Seoul 05029, Korea; (J.Y.L.); (E.J.); (H.Y.); (S.S.A.)
| | - Hyunjin Yeo
- Department of Biological Sciences, Sanghuh College of Lifesciences, Konkuk University, Seoul 05029, Korea; (J.Y.L.); (E.J.); (H.Y.); (S.S.A.)
| | - Sung Shin Ahn
- Department of Biological Sciences, Sanghuh College of Lifesciences, Konkuk University, Seoul 05029, Korea; (J.Y.L.); (E.J.); (H.Y.); (S.S.A.)
| | - Yoongho Lim
- Division of Bioscience and Biotechnology, BMIC, Konkuk University, Seoul 05029, Korea;
| | - Young Han Lee
- Department of Biological Sciences, Sanghuh College of Lifesciences, Konkuk University, Seoul 05029, Korea; (J.Y.L.); (E.J.); (H.Y.); (S.S.A.)
- Cancer and Metabolism Institute, Konkuk University, Seoul 05029, Korea
- Correspondence: ; Tel.: +82-2-2049-6115
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27
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Fagiani F, Di Marino D, Romagnoli A, Travelli C, Voltan D, Mannelli LDC, Racchi M, Govoni S, Lanni C. Molecular regulations of circadian rhythm and implications for physiology and diseases. Signal Transduct Target Ther 2022; 7:41. [PMID: 35136018 PMCID: PMC8825842 DOI: 10.1038/s41392-022-00899-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/11/2022] Open
Abstract
The term “circadian rhythms” describes endogenous oscillations with ca. 24-h period associated with the earth’s daily rotation and light/dark cycle. Such rhythms reflect the existence of an intrinsic circadian clock that temporally orchestrates physiological processes to adapt the internal environment with the external cues. At the molecular level, the circadian clock consists of multiple sets of transcription factors resulting in autoregulatory transcription-translation feedback loops. Notably, in addition to their primary role as generator of circadian rhythm, the biological clock plays a key role in controlling physiological functions of almost all tissues and organs. It regulates several intracellular signaling pathways, ranging from cell proliferation, DNA damage repair and response, angiogenesis, metabolic and redox homeostasis, to inflammatory and immune response. In this review, we summarize findings showing the crosstalk between the circadian molecular clock and some key intracellular pathways, describing a scenario wherein their reciprocal regulation impinges upon several aspects of mammalian physiology. Moreover, based on evidence indicating that circadian rhythms can be challenged by environmental factors, social behaviors, as well as pre-existing pathological conditions, we discuss implications of circadian misalignment in human pathologies, such as cancer and inflammatory diseases. Accordingly, disruption of circadian rhythm has been reported to affect several physiological processes that are relevant to human diseases. Expanding our understanding of this field represents an intriguing and transversal medicine challenge in order to establish a circadian precision medicine.
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Affiliation(s)
- Francesca Fagiani
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Cristina Travelli
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Davide Voltan
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | | | - Marco Racchi
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Stefano Govoni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Cristina Lanni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy.
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28
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Wu Y, Jiao Y, Zhao Y, Jia H, Xu L. Noise-induced quasiperiod and period switching. Phys Rev E 2022; 105:014419. [PMID: 35193235 DOI: 10.1103/physreve.105.014419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
We employ a typical genetic circuit model to explore how noise can influence dynamic structure. With the increase of a key interactive parameter, the model will deterministically go through two bifurcations and three dynamic structure regions. We find that a quasiperiodic component, which is not allowed by deterministic dynamics, will be generated by noise inducing in the first two regions, and this quasiperiod will be more and more stable along with the increase in noise. In particular, in the second region the quasiperiod will compete with a stable limit cycle and perform a new transient rhythm. Furthermore, we ascertain the entropy production rate and the heat dissipation rate, and discover a minimal value with theoretical elucidation. In the end, we unveil the mechanism of the formation of quasiperiods, and show a practical biological example. We expect this work to be helpful in solving some biological or ecological problems, such as the genetic origin of periodical cicadas and population dynamics with fluctuation.
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Affiliation(s)
- Yuxuan Wu
- Biophysics & Complex System Center, Center of Theoretical Physics, College of Physics, Jilin University Changchun 130012, People's Republic of China
| | - Yuxing Jiao
- Biophysics & Complex System Center, Center of Theoretical Physics, College of Physics, Jilin University Changchun 130012, People's Republic of China
| | - Yanzhen Zhao
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | - Haojun Jia
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Liufang Xu
- Biophysics & Complex System Center, Center of Theoretical Physics, College of Physics, Jilin University Changchun 130012, People's Republic of China
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29
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Shiraishi R, Morita S, Goto Y, Mizoguchi Y, Nakamura W, Nakamura TJ. Diurnal variations of triglyceride accumulation in mouse and bovine adipocyte-derived cell lines. Anim Sci J 2022; 93:e13802. [PMID: 36562279 DOI: 10.1111/asj.13802] [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: 04/06/2022] [Revised: 11/04/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
Several studies have suggested a strong interaction between the circadian clock and lipid metabolism in mammals. The circadian clock is driven by endogenous cyclic gene expression patterns, commonly referred to as clock genes, and transcription-translation negative feedback loops. Clock genes regulate the transcription of some lipid metabolism-related genes; however, the relationship between the circadian clock and triglyceride (TG) accumulation at the cellular level remains unclear. Here, we evaluated rhythms of intracellular TG accumulation levels as well as the expression of clock genes and lipid metabolism-related genes for 54 h in mouse and bovine adipose-derived cell cultures. To the best of our knowledge, this study represents the first report demonstrating that TG accumulation exhibits diurnal variations, with the pattern differing among cell types. Furthermore, we found that expression of clock genes and corresponding lipid metabolism-related genes exhibited circadian rhythms. Our results suggest that the cellular clock regulates lipid metabolism-related genes to relate circadian rhythms of TG accumulation in each cell type. We anticipate that the amount of fat stored depends on the timing of the supply of glucose-the precursor of fat. The findings of this study will contribute to the advancement of chrono-nutrition.
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Affiliation(s)
- Rena Shiraishi
- Laboratory of Animal Physiology, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Satomi Morita
- Laboratory of Animal Physiology, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Yoshikuni Goto
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Tokyo, Japan
| | - Yasushi Mizoguchi
- Laboratory of Animal Genetics, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Wataru Nakamura
- Department of Oral-Chrono Physiology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Takahiro J Nakamura
- Laboratory of Animal Physiology, School of Agriculture, Meiji University, Kawasaki, Japan
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30
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Deans C. Biological Prescience: The Role of Anticipation in Organismal Processes. Front Physiol 2021; 12:672457. [PMID: 34975512 PMCID: PMC8719636 DOI: 10.3389/fphys.2021.672457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 11/18/2021] [Indexed: 11/13/2022] Open
Abstract
Anticipation is the act of using information about the past and present to make predictions about future scenarios. As a concept, it is predominantly associated with the psychology of the human mind; however, there is accumulating evidence that diverse taxa without complex neural systems, and even biochemical networks themselves, can respond to perceived future conditions. Although anticipatory processes, such as circadian rhythms, stress priming, and cephalic responses, have been extensively studied over the last three centuries, newer research on anticipatory genetic networks in microbial species shows that anticipatory processes are widespread, evolutionarily old, and not simply reserved for neurological complex organisms. Overall, data suggest that anticipatory responses represent a unique type of biological processes that can be distinguished based on their organizational properties and mechanisms. Unfortunately, an empirically based biologically explicit framework for describing anticipatory processes does not currently exist. This review attempts to fill this void by discussing the existing examples of anticipatory processes in non-cognitive organisms, providing potential criteria for defining anticipatory processes, as well as their putative mechanisms, and drawing attention to the often-overlooked role of anticipation in the evolution of physiological systems. Ultimately, a case is made for incorporating an anticipatory framework into the existing physiological paradigm to advance our understanding of complex biological processes.
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Affiliation(s)
- Carrie Deans
- Entomology Department, University of Minnesota, St. Paul, MN, United States
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31
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Yan J, Li S, Kim YJ, Zeng Q, Radziejwoski A, Wang L, Nomura Y, Nakagami H, Somers DE. TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth. EMBO J 2021; 40:e108684. [PMID: 34726281 DOI: 10.15252/embj.2021108684] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post-translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho-mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho-mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre-dawn hypocotyl growth-related genes (PHGs), leading to a net de-repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF-YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF-TOC1) acts as a transcriptional co-repressor with HDA15 to inhibit PIF-mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co-regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth.
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Affiliation(s)
- Jiapei Yan
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Shibai Li
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,Memorial Sloan Kettering Cancer Center, Molecular Biology Program, New York, NY, USA
| | - Yeon Jeong Kim
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Qingning Zeng
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | | | - Lei Wang
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,The Chinese Academy of Sciences, Institute of Botany, Beijing, China
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan.,Max Planck Institute for Plant Breeding Research, Protein Mass Spectrometry, Cologne, Germany
| | - David E Somers
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,POSTECH, Division of Integrative Biosciences and Biotechnology, Pohang, South Korea
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32
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Zhang Y, Zhang W, Liu C. Integration of peripheral circadian clock and energy metabolism in metabolic tissues. J Mol Cell Biol 2021; 12:481-485. [PMID: 31863090 PMCID: PMC7493026 DOI: 10.1093/jmcb/mjz112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 06/24/2019] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yanchen Zhang
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Wenxiang Zhang
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines and School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
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33
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Pei J, Xu Y, Zong S, Ren L. Transcriptomic and Metabolomic Data Reveal the Key Metabolic Pathways Affecting Streltzoviella insularis (Staudinger) (Lepidoptera: Cossidae) Larvae During Overwintering. Front Physiol 2021; 12:655059. [PMID: 34220530 PMCID: PMC8250450 DOI: 10.3389/fphys.2021.655059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/13/2021] [Indexed: 12/25/2022] Open
Abstract
Streltzoviella insularis (Staudinger) (Lepidoptera: Cossidae) is a woodboring insect feeding on Fraxinus pennsylvanica, Sophora japonica, and Ginkgo biloba, as well as many other species used for urban greening and plain afforestation in northern China, including the temperate north. There is also a risk that S. insularis could spread through the transportation of seedlings, thereby increasing urban greening costs. However, how S. insularis increases the cold tolerance then reduces it to survive winter temperature below 0°C remains unclear. In the transcriptomic of S. insularis, we identified three profiles (profile 25, 27, and 13) whose trends related to the cold tolerance. We detected 1,783 differentially expressed genes (in profile 25) and identified 522 genes enriched in the AMPK signaling pathway. The metabolome analysis identified 122 differential metabolites. We identified four co-pathways, among which "Glycerophospholipid metabolism" was the pathway most enriched in differentially expressed genes and differential metabolites. The AMPK signaling and glycerophospholipid metabolism pathways play key roles in the natural overwintering physiological process of S. insularis larvae.
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Affiliation(s)
| | | | - Shixiang Zong
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
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34
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Zhang J, Sun R, Jiang T, Yang G, Chen L. Circadian Blood Pressure Rhythm in Cardiovascular and Renal Health and Disease. Biomolecules 2021; 11:biom11060868. [PMID: 34207942 PMCID: PMC8230716 DOI: 10.3390/biom11060868] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 12/21/2022] Open
Abstract
Blood pressure (BP) follows a circadian rhythm, it increases on waking in the morning and decreases during sleeping at night. Disruption of the circadian BP rhythm has been reported to be associated with worsened cardiovascular and renal outcomes, however the underlying molecular mechanisms are still not clear. In this review, we briefly summarized the current understanding of the circadian BP regulation and provided therapeutic overview of the relationship between circadian BP rhythm and cardiovascular and renal health and disease.
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Affiliation(s)
- Jiayang Zhang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China; (J.Z.); (R.S.); (T.J.)
| | - Ruoyu Sun
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China; (J.Z.); (R.S.); (T.J.)
| | - Tingting Jiang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China; (J.Z.); (R.S.); (T.J.)
| | - Guangrui Yang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
| | - Lihong Chen
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian 116044, China; (J.Z.); (R.S.); (T.J.)
- Correspondence: ; Tel.: +86-411-86118984
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35
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Lin J, Gao L, Lin Y, Wang S, Yang Z, Ren S, Chen M, Wu B. Pharmacokinetics-Based Chronoefficacy of Semen Strychni and Tripterygium Glycoside Tablet Against Rheumatoid Arthritis. Front Pharmacol 2021; 12:673263. [PMID: 34108880 PMCID: PMC8181759 DOI: 10.3389/fphar.2021.673263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 11/21/2022] Open
Abstract
Rheumatoid arthritis is a systemic autoimmune disease characterized by synovial inflammation and bone destruction. Identifying drugs with time-varying efficacy and toxicity, and elucidating the mechanisms would help to improve treatment efficacy and reduce adverse effects. Here, we aimed to determine the chronoefficacy of semen strychni (SS) and tripterygium glycoside tablet (TGT) against rheumatoid arthritis in mice, and to investigate a potential role of circadian pharmacokinetics in generating chronoefficacy. SS extract and TGT suspension were prepared with ultrasonication. Effects of SS and TGT on collagen-induced arthritis (CIA) were evaluated by measuring TNF-α and IL-6 levels. SS dosed at ZT18 was more effective in protecting against CIA than drug dosed at ZT6 (i.e., lower levels of key inflammatory factors at ZT18 than at ZT6). This was accompanied by higher systemic exposure levels of strychnine and brucine (two main putative active ingredients of SS) in ZT18-treated than in ZT6-treated CIA mice. TGT dosing at ZT2 showed a better efficacy against CIA as compared to herb doing at ZT14. Consistently, ZT2 dosing generated a higher exposure of triptolide (a main putative active ingredient of TGT) as compared to ZT14 dosing in CIA mice. Moreover, strychnine, brucine, and triptolide significantly inhibited the proliferation of fibroblast-like synoviocytes, and reduced the production of TNF-α and IL-6 and the mRNAs of TNF-α, IL-6, COX-2, and iNOS, suggesting that they possessed an anti-arthritis activity. In conclusion, SS and TGT display chronoefficacy against rheumatoid arthritis in mice, that is attributed to circadian pharmacokinetics of main active ingredients. Our findings have implications for improving treatment outcomes of SS and TGT via timed delivery.
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Affiliation(s)
- Jingpan Lin
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lu Gao
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yanke Lin
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuai Wang
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zemin Yang
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shujing Ren
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Min Chen
- College of Pharmacy, Jinan University, Guangzhou, China.,Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Baojian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
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Sujino M, Koinuma S, Minami Y, Shigeyoshi Y. Heavy Water Lengthens the Molecular Circadian Clock Period in the Suprachiasmatic Nucleus of Mice In Vitro. J Biol Rhythms 2021; 36:410-418. [PMID: 33969745 DOI: 10.1177/07487304211012905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Heavy water lengthens the periods of circadian rhythms in various plant and animal species. Many studies have reported that drinking heavy water lengthens the periods of circadian activity rhythms of rodents by slowing the clock mechanism in the suprachiasmatic nucleus (SCN), the mammalian circadian center. The SCN clock is stable and robust against disturbance, due to its intercellular network. It is unclear whether this robustness provides resistance to the effects of heavy water. Here, we report that heavy water lengthened the rhythm period of clock gene expression of the SCN and peripheral tissues in vitro using a PERIOD2::LUCIFERASE bioluminescence reporter. Our results show that the period-elongation rate of the SCN is similar to those of other tissues. Therefore, the intercellular network of the SCN is not resistant to the period-elongation effect of heavy water.
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Affiliation(s)
- Mitsugu Sujino
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, Osakasayama, Japan
| | - Satoshi Koinuma
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, Osakasayama, Japan
| | - Yoichi Minami
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, Osakasayama, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Faculty of Medicine, Kindai University, Osakasayama, Japan
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Meher PK, Mohapatra A, Satpathy S, Sharma A, Saini I, Pradhan SK, Rai A. PredCRG: A computational method for recognition of plant circadian genes by employing support vector machine with Laplace kernel. PLANT METHODS 2021; 17:46. [PMID: 33902670 PMCID: PMC8074503 DOI: 10.1186/s13007-021-00744-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Circadian rhythms regulate several physiological and developmental processes of plants. Hence, the identification of genes with the underlying circadian rhythmic features is pivotal. Though computational methods have been developed for the identification of circadian genes, all these methods are based on gene expression datasets. In other words, we failed to search any sequence-based model, and that motivated us to deploy the present computational method to identify the proteins encoded by the circadian genes. RESULTS Support vector machine (SVM) with seven kernels, i.e., linear, polynomial, radial, sigmoid, hyperbolic, Bessel and Laplace was utilized for prediction by employing compositional, transitional and physico-chemical features. Higher accuracy of 62.48% was achieved with the Laplace kernel, following the fivefold cross- validation approach. The developed model further secured 62.96% accuracy with an independent dataset. The SVM also outperformed other state-of-art machine learning algorithms, i.e., Random Forest, Bagging, AdaBoost, XGBoost and LASSO. We also performed proteome-wide identification of circadian proteins in two cereal crops namely, Oryza sativa and Sorghum bicolor, followed by the functional annotation of the predicted circadian proteins with Gene Ontology (GO) terms. CONCLUSIONS To the best of our knowledge, this is the first computational method to identify the circadian genes with the sequence data. Based on the proposed method, we have developed an R-package PredCRG ( https://cran.r-project.org/web/packages/PredCRG/index.html ) for the scientific community for proteome-wide identification of circadian genes. The present study supplements the existing computational methods as well as wet-lab experiments for the recognition of circadian genes.
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Affiliation(s)
| | - Ansuman Mohapatra
- Orissa University of Agriculture and Technology, Bhubaneswar, Odisha India
| | - Subhrajit Satpathy
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anuj Sharma
- Uttarakhand Council for Biotechnology, Pantnagar, Uttarakhand India
| | - Isha Saini
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Gao Y, Wu Y, Zhang N, Yuan H, Wang F, Xu H, Yu J, Ma J, Hou S, Cao X. IDH1 gene mutation activates Smad signaling molecules to regulate the expression levels of cell cycle and biological rhythm genes in human glioma U87‑MG cells. Mol Med Rep 2021; 23:354. [PMID: 33760141 PMCID: PMC7974315 DOI: 10.3892/mmr.2021.11993] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/09/2021] [Indexed: 02/07/2023] Open
Abstract
Isocitrate dehydrogenase1 (IDH1) mutation is the most important genetic change in glioma. The most common IDH1 mutation results in the amino acid substitution of arginine 132 (Arg/R132), which is located at the active site of the enzyme. IDH1 Arg132His (R132H) mutation can reduce the proliferative rate of glioma cells. Numerous diseases follow circadian rhythms, and there is growing evidence that circadian disruption may be a risk factor for cancer in humans. Dysregulation of the circadian clock serves an important role in the development of malignant tumors, including glioma. Brain-Muscle Arnt-Like protein 1 (BMAL1) and Circadian Locomotor Output Cycles Kaput (CLOCK) are the main biological rhythm genes. The present study aimed to further study whether there is an association between IDH1 R132H mutation and biological rhythm in glioma, and whether this affects the occurrence of glioma. The Cancer Genome Atlas (TCGA) database was used to detect the expression levels of the biological rhythm genes BMAL1 and CLOCK in various types of tumor. Additionally, U87-MG cells were infected with wild-type and mutant IDH1 lentiviruses. Colony formation experiments were used to detect cell proliferation in each group, cell cycle distribution was detected by flow cytometry and western blotting was used to detect the expression levels of wild-type and mutant IDH1, cyclins, biological rhythm genes and Smad signaling pathway-associated genes in U87-MG cells. TCGA database results suggested that BMAL1 and CLOCK were abnormally expressed in glioma. Cells were successfully infected with wild-type and mutant IDH1 lentiviruses. Colony formation assay revealed decreased cell proliferation in the IDH1 R132H mutant group. The cell cycle distribution detected by flow cytometry indicated that IDH1 gene mutation increased the G1 phase ratio and decreased the S phase ratio in U87-MG cells. The western blotting results demonstrated that IDH1 R132H mutation decreased the expression levels of the S phase-associated proteins Cyclin A and CDK2, and increased the expression levels of the G1 phase-associated proteins Cyclin D3 and CDK4, but did not significantly change the expression levels of the G2/M phase-associated protein Cyclin B1. The expression levels of the positive and negative rhythm regulation genes BMAL1, CLOCK, period (PER s (PER1, 2 and 3) and cryptochrom (CRY)s (CRY1 and 2) were significantly decreased, those of the Smad signaling pathway-associated genes Smad2, Smad3 and Smad2-3 were decreased, and those of phosphorylated (p)-Smad2, p-Smad3 and Smad4 were increased. Therefore, the present results suggested that the IDH1 R132H mutation may alter the cell cycle and biological rhythm genes in U87-MG cells through the TGF-β/Smad signaling pathway.
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Affiliation(s)
- Yongying Gao
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Yanwei Wu
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Ningmei Zhang
- Department of Pathology, Tumor Hospital, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Hongmei Yuan
- Functional Department, Ningxia Hui Autonomous Region People's Hospital, Yinchuan, Ningxia 750021, P.R. China
| | - Fei Wang
- Department of Pathology, The First People's Hospital of Yinchuan, Yinchuan, Ningxia 750001, P.R. China
| | - Hui Xu
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Jiaxiang Yu
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Jie Ma
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Shaozhang Hou
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Xiangmei Cao
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
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Wake-sleep cycles are severely disrupted by diseases affecting cytoplasmic homeostasis. Proc Natl Acad Sci U S A 2020; 117:28402-28411. [PMID: 33106420 PMCID: PMC7668169 DOI: 10.1073/pnas.2003524117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circadian rhythms including wake-sleep cycles are driven by molecular time cues generated by a self-sustaining transcriptional negative feedback loop. Among all clock proteins, PERIOD (PER) is considered the pacemaker protein because its rhythm of accumulation and nuclear entry generates the timing and duration of feedback inhibition. Here we provide a new understanding of how robust PER rhythms are generated: the collective action of interacting PER molecules, not a random mass action of individual molecules, allows compensation of spatial and temporal differences (or “noise”) of individual molecules. We also show that the collective PER rhythm requires healthy cytoplasmic trafficking, and that circadian sleep disorders can arise in such conditions as obesity, aging, and neurodegenerative disorders in which the cytoplasm becomes congested. The circadian clock is based on a transcriptional feedback loop with an essential time delay before feedback inhibition. Previous work has shown that PERIOD (PER) proteins generate circadian time cues through rhythmic nuclear accumulation of the inhibitor complex and subsequent interaction with the activator complex in the feedback loop. Although this temporal manifestation of the feedback inhibition is the direct consequence of PER’s cytoplasmic trafficking before nuclear entry, how this spatial regulation of the pacemaker affects circadian timing has been largely unexplored. Here we show that circadian rhythms, including wake-sleep cycles, are lengthened and severely unstable if the cytoplasmic trafficking of PER is disrupted by any disease condition that leads to increased congestion in the cytoplasm. Furthermore, we found that the time delay and robustness in the circadian clock are seamlessly generated by delayed and collective phosphorylation of PER molecules, followed by synchronous nuclear entry. These results provide clear mechanistic insight into why circadian and sleep disorders arise in such clinical conditions as metabolic and neurodegenerative diseases and aging, in which the cytoplasm is congested.
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Malaguarnera R, Ledda C, Filippello A, Frasca F, Francavilla VC, Ramaci T, Parisi MC, Rapisarda V, Piro S. Thyroid Cancer and Circadian Clock Disruption. Cancers (Basel) 2020; 12:E3109. [PMID: 33114365 PMCID: PMC7690860 DOI: 10.3390/cancers12113109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/18/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Thyroid cancer (TC) represents the most common malignancy of the endocrine system, with an increased incidence across continents attributable to both improvement of diagnostic procedures and environmental factors. Among the modifiable risk factors, insulin resistance might influence the development of TC. A relationship between circadian clock machinery disfunction and TC has recently been proposed. The circadian clock machinery comprises a set of rhythmically expressed genes responsible for circadian rhythms. Perturbation of this system contributes to the development of pathological states such as cancer. Several clock genes have been found deregulated upon thyroid nodule malignant transformation. The molecular mechanisms linking circadian clock disruption and TC are still unknown but could include insulin resistance. Circadian misalignment occurring during shift work, jet lag, high fat food intake, is associated with increased insulin resistance. This metabolic alteration, in turn, is associated with a well-known risk factor for TC i.e., hyperthyrotropinemia, which could also be induced by sleep disturbances. In this review, we describe the mechanisms controlling the circadian clock function and its involvement in the cell cycle, stemness and cancer. Moreover, we discuss the evidence supporting the link between circadian clockwork disruption and TC development/progression, highlighting its potential implications for TC prevention, diagnosis and therapy.
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Affiliation(s)
- Roberta Malaguarnera
- School of Human and Social Sciences, “Kore” University of Enna, 94100 Enna, Italy; (R.M.); (V.C.F.); (T.R.); (M.C.P.)
| | - Caterina Ledda
- Department of Clinical and Experimental Medicine, Occupational Medicine, University of Catania, 95100 Catania, Italy;
| | - Agnese Filippello
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (A.F.); (S.P.)
| | - Francesco Frasca
- Endocrinology Unit, Department of Clinical and Experimental Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy;
| | - Vincenzo Cristian Francavilla
- School of Human and Social Sciences, “Kore” University of Enna, 94100 Enna, Italy; (R.M.); (V.C.F.); (T.R.); (M.C.P.)
| | - Tiziana Ramaci
- School of Human and Social Sciences, “Kore” University of Enna, 94100 Enna, Italy; (R.M.); (V.C.F.); (T.R.); (M.C.P.)
| | - Maria Chiara Parisi
- School of Human and Social Sciences, “Kore” University of Enna, 94100 Enna, Italy; (R.M.); (V.C.F.); (T.R.); (M.C.P.)
| | - Venerando Rapisarda
- Department of Clinical and Experimental Medicine, Occupational Medicine, University of Catania, 95100 Catania, Italy;
| | - Salvatore Piro
- Department of Clinical and Experimental Medicine, Internal Medicine, Garibaldi-Nesima Hospital, University of Catania, 95122 Catania, Italy; (A.F.); (S.P.)
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Deshpande RP, Sharma S, Watabe K. The Confounders of Cancer Immunotherapy: Roles of Lifestyle, Metabolic Disorders and Sociological Factors. Cancers (Basel) 2020; 12:E2983. [PMID: 33076303 PMCID: PMC7602474 DOI: 10.3390/cancers12102983] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023] Open
Abstract
Checkpoint blockade immunotherapy (CPI) is an effective treatment option for many types of cancers. Irrespective of its wide clinical implications, the overall efficacy remains unpredictable and even poor in certain pathologies such as breast cancer. Thus, it is imperative to understand the role of factors affecting its responsiveness. In this review, we provide an overview on the involvement of sociological factors, lifestyles and metabolic disorders in modulating the CPI response in patients from multiple malignancies. Lifestyle habits including exercise, and diet promoted therapeutic responsiveness while alcohol consumption mitigated the CPI effect by decreasing mutational burden and hampering antigen presentation by dendritic cells. Metabolic disorder such as obesity was recognized to enhance the PD-1 expression while diabetes and hypertension were consequences of CPI therapy rather than causes. Among the sociologic factors, sex and race positively influenced the CPI effectiveness on account of increased effector T cell activity and increased PD-1 expression while ageing impaired CPI responsiveness by decreasing functional T cell and increased toxicity. The combined effect of these factors was observed for obesity and gender, in which obese males had the most significant effect of CPI. Therefore these variables should be carefully considered before treating patients with CPI for optimal treatment outcome.
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Affiliation(s)
| | | | - Kounosuke Watabe
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Winston-Salem, NC 27157, USA; (R.P.D.); (S.S.)
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Romanowski A, Schlaen RG, Perez-Santangelo S, Mancini E, Yanovsky MJ. Global transcriptome analysis reveals circadian control of splicing events in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:889-902. [PMID: 32314836 DOI: 10.1111/tpj.14776] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 05/21/2023]
Abstract
The circadian clock of Arabidopsis thaliana controls many physiological and molecular processes, allowing plants to anticipate daily changes in their environment. However, developing a detailed understanding of how oscillations in mRNA levels are connected to oscillations in co/post-transcriptional processes, such as splicing, has remained a challenge. Here we applied a combined approach using deep transcriptome sequencing and bioinformatics tools to identify novel circadian-regulated genes and splicing events. Using a stringent approach, we identified 300 intron retention, eight exon skipping, 79 alternative 3' splice site usage, 48 alternative 5' splice site usage, and 350 multiple (more than one event type) annotated events under circadian regulation. We also found seven and 721 novel alternative exonic and intronic events. Depletion of the circadian-regulated splicing factor AtSPF30 homologue resulted in the disruption of a subset of clock-controlled splicing events. Altogether, our global circadian RNA-seq coupled with an in silico, event-centred, splicing analysis tool offers a new approach for studying the interplay between the circadian clock and the splicing machinery at a global scale. The identification of many circadian-regulated splicing events broadens our current understanding of the level of control that the circadian clock has over this co/post-transcriptional regulatory layer.
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Affiliation(s)
- Andrés Romanowski
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Rubén G Schlaen
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Soledad Perez-Santangelo
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Estefanía Mancini
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
| | - Marcelo J Yanovsky
- Comparative Genomics of Plant Development, Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1405BWE, Buenos Aires, Argentina
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The circadian clock gene Bmal1 facilitates cisplatin-induced renal injury and hepatization. Cell Death Dis 2020; 11:446. [PMID: 32522976 PMCID: PMC7287064 DOI: 10.1038/s41419-020-2655-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/13/2022]
Abstract
Cisplatin is one of the most potent chemotherapy drugs to treat cancers, but its clinical application remains limited due to severe nephrotoxicity. Several approaches have been developed to minimize such side effects, notably including chronotherapy, a well-known strategy based on the circadian clock. However, the component of the circadian clock machinery that particularly responses to the cisplatin stimulation remains unknown, including its functions in cisplatin-induced renal injury. In our present study, we demonstrated that Bmal1, as a key clock gene, was induced by the cisplatin stimulation in the mouse kidney and cultured human HK-2 renal cells. Gain- and loss-of-function studies indicated that Bmal1 facilitated cisplatin-induced renal injury both in vivo and in vitro, by aggravating the cell apoptotic process. More importantly, RNA-seq analysis revealed that Bmal1 triggered the expression of hallmark genes involved in renal hepatization, a critical event accompanied by the injury. At the molecular level, Bmal1 activated the transcription of hepatization-associated genes through direct recruitment to the E-box motifs of their promoters. Our findings suggest that Bmal1, a pivotal mediator induced renal injury in response to cisplatin treatment, and the therapeutic intervention targeting Bmal1 in the kidney may be a promising strategy to minimize the toxic side-effects of cisplatin in its clinical applications.
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Thermal stability analyses of human PERIOD-2 C-terminal domain using dynamic light scattering and circular dichroism. PLoS One 2020; 15:e0221180. [PMID: 32320392 PMCID: PMC7176140 DOI: 10.1371/journal.pone.0221180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 03/18/2020] [Indexed: 11/23/2022] Open
Abstract
At the molecular level, the circadian clock is regulated by a time delayed transcriptional-translational feedback loop in which the core proteins interact with each other rhythmically to drive daily biological rhythms. The C-terminal domain of a key clock protein PER2 (PER2c) plays a critically important role in the loop, not only for its interaction with the binding partner CRY proteins but also for the CRY/PER complex’s translocation from the cytosol to the nucleus. Previous circular dichroism (CD) spectroscopic studies have shown that mouse PER2c (mPER2c) is less structured in solution by itself but folded into stable secondary structures upon interaction with mouse CRYs. To understand the stability and folding of human PER2c (hPER2c), we expressed and purified hPER2c. Three oligomerization forms of recombinant hPER2c were identified and thoroughly characterized through a combination of biochemical and biophysical techniques. Different to mPER2c, both thermal unfolding DLS and CD analyses suggested that all forms of hPER2c have very stable secondary structures in solution by themselves with melting temperatures higher than the physiological body temperature, indicating that hPER2c does not require CRY to fold. Furthermore, we examined the effects of EDTA, salt concentration, and a reducing agent on hPER2c folding and oligomerization. The ability of hPER2c forming oligomers reflects the potential role of hPER2c in the assembly of circadian rhythm core protein complexes.
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Abstract
Cellular differentiation is a common underlying feature of all multicellular organisms through which naïve cells progressively become fate restricted and develop into mature cells with specialized functions. A comprehensive understanding of the regulatory mechanisms of cell fate choices during de- velopment, regeneration, homeostasis, and disease is a central goal of mod- ern biology. Ongoing rapid advances in single-cell biology are enabling the exploration of cell fate specification at unprecedented resolution. Here, we review single-cell RNA sequencing and sequencing of other modalities as methods to elucidate the molecular underpinnings of lineage specification. We specifically discuss how the computational tools available to reconstruct lineage trajectories, quantify cell fate bias, and perform dimensionality re- duction for data visualization are providing new mechanistic insights into the process of cell fate decision. Studying cellular differentiation using single- cell genomic tools is paving the way for a detailed understanding of cellular behavior in health and disease.
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Affiliation(s)
- Sagar
- Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany
| | - Dominic Grün
- Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.,CIBSS (Centre for Integrative Biological Signaling Studies), University of Freiburg, D-79104 Freiburg, Germany
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An J, Yu D, Yang X, Rong X, Han B, Yang C, Yang Y, Zhou H, Li T. Combined transcriptome sequencing reveals the photoperiod insensitivity mechanism of oats. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 146:133-142. [PMID: 31751913 DOI: 10.1016/j.plaphy.2019.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/01/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
Avena sativa L. is the most important cultivated oat species worldwide. Although photoperiod-insensitive oat varieties exist, the molecular mechanisms underlying their photoperiod sensitivity are poorly understood. This study investigated the effects of day length on the fioral transition of oats and the mechanisms underlying oat photoperiod insensitivity. Photoperiod-sensitive and photoperiod-insensitive varieties, including gp012, were used in shading experiments, and the developing leaves and main shoot apices (MSAs) of the HONGQI2 and gp012 varieties were used for sequencing. Leaves and MSAs were collected in 2016, and their transcriptomes were sequenced. The photoperiod-insensitive varieties headed under both short-day and long-day conditions, while the photoperiod-sensitive varieties headed only under long-day conditions. A total of 60673 transcript sequences were obtained, 7932 of which were differentially expressed; 3194 and 4738 transcripts were differentially expressed in the leaves and MSAs, respectively. A total of 25793 transcripts were classified into 123 pathways based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The carbon metabolism pathways were dominant, followed by ribosome and protein processing in the endoplasmic reticulum. In addition, 203 transcripts were classified into the circadian rhythm pathway. Compared with the expression of pseudo-response regulator protein 37 (PRR37) in photoperiod-sensitive varieties, that in photoperiod-insensitive varieties was upregulated. Among the differentially expressed transcripts (DETs), 8 MADS-box genes were identified. PRR37 is a key regulator of oat photoperiod insensitivity. The obtained transcriptome dataset may provide a reference for analyzing oat transcript expression, and the results should be used as a reference for oat breeding and production.
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Affiliation(s)
- Jianghong An
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Dongyang Yu
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Xiaohong Yang
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China.
| | - Xiaoping Rong
- Inner Mongolian Agro-technical Extension Station, Hohhot, 010010, China.
| | - Bing Han
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Cai Yang
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China.
| | - Yan Yang
- College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, 010018, China.
| | - Haitao Zhou
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China.
| | - Tianliang Li
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China.
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Rosenberg Y, Doniger T, Harii S, Sinniger F, Levy O. Demystifying Circalunar and Diel Rhythmicity in Acropora digitifera under Constant Dim Light. iScience 2019; 22:477-488. [PMID: 31835172 PMCID: PMC6926284 DOI: 10.1016/j.isci.2019.11.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/22/2019] [Accepted: 11/22/2019] [Indexed: 01/09/2023] Open
Abstract
Life on earth has evolved under constant environmental changes; in response to these changes, most organisms have developed an endogenous clock that allows them to anticipate daily and seasonal changes and adapt their biology accordingly. Light cycles synchronize biological rhythms and are controlled by an endogenous clock that is entrained by environmental cues. Light is known to play a key role in the biology of symbiotic corals as they exhibit many biological processes entrained by daily light patterns. In this study, we aimed at determining the effect of constant dim light on coral's perception of diel and monthly cycles. Our results show that under constant dim light corals display a loss of rhythmic processes and constant stimuli by light, which initiates signal transduction that results in an abnormal cell cycle, cell proliferation, and protein synthesis. The results emphasize how constant dim light can mask the biological clock of Acropora digitifera. Light entrains many biological processes governed by the endogenous clock Constant dim light overrides the biological clock of A. digitifera corals Artificial light impacts the processes that allow corals to thrive in our oceans The increase of artificial light in coastal areas is a growing threat to coral reefs
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Affiliation(s)
- Yael Rosenberg
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel.
| | - Tirza Doniger
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Saki Harii
- Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Frederic Sinniger
- Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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Wu Y, Tao B, Zhang T, Fan Y, Mao R. Pan-Cancer Analysis Reveals Disrupted Circadian Clock Associates With T Cell Exhaustion. Front Immunol 2019; 10:2451. [PMID: 31708917 PMCID: PMC6821711 DOI: 10.3389/fimmu.2019.02451] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022] Open
Abstract
Although dysfunctional circadian clock has emerged as a hallmark of cancer, fundamental gaps remain in our understanding of the underlying mechanisms involved. Here, we systematically analyze the core genes of the circadian clock (CLOCK, ARNTL, ARNTL2, NPAS2, NR1D1, NR1D2, CRY1, CRY2, RORA, RORB, RORC, PER1, PER2, and PER3) across a broad range of cancers. To our surprise, core negative regulators (PER1, PER2, PER3, CRY1, and CRY2) are consistently downregulated, while core positive regulators show minimal alterations, indicating disrupted circadian clock in cancers. Such downregulation originates from copy number variations where heterozygous deletion predominates. The disrupted circadian clock is significantly associated with patient outcome. Further pathway enrichment analysis suggests that the circadian clock widely impacts 45 pathways such as the Ras signaling pathway and T cell receptor signaling pathway. By using state-of-the-art immune cell deconvolution and pathway quantification, we demonstrate that abnormal circadian clock contributes to T cell exhaustion and global upregulation of immune inhibitory molecules such as PD-L1 and CTLA-4. In summary, the rhythm of the circadian clock is disrupted in cancers. Abnormal circadian clock linked with immune evasion may serve as a potential hallmark of cancer.
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Affiliation(s)
- Yingcheng Wu
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu, China
| | - Baorui Tao
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu, China.,Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Tianyang Zhang
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
| | - Yihui Fan
- Laboratory of Medical Science, School of Medicine, Nantong University, Jiangsu, China.,Department of Immunology, School of Medicine, Nantong University, Jiangsu, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Jiangsu, China
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50
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Lee SJ, Morse D, Hijri M. Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms. MYCORRHIZA 2019; 29:403-412. [PMID: 31190278 DOI: 10.1007/s00572-019-00903-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/05/2019] [Indexed: 06/09/2023]
Abstract
Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.
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Affiliation(s)
- Soon-Jae Lee
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - David Morse
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale (IRBV), Université de Montréal, 4101 Rue Sherbrooke Est, Montréal, Québec, H1X 2B2, Canada.
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