1
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Butler CT, Rodgers AM, Curtis AM, Donnelly RF. Chrono-tailored drug delivery systems: recent advances and future directions. Drug Deliv Transl Res 2024; 14:1756-1775. [PMID: 38416386 PMCID: PMC11153310 DOI: 10.1007/s13346-024-01539-4] [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] [Accepted: 02/07/2024] [Indexed: 02/29/2024]
Abstract
Circadian rhythms influence a range of biological processes within the body, with the central clock or suprachiasmatic nucleus (SCN) in the brain synchronising peripheral clocks around the body. These clocks are regulated by external cues, the most influential being the light/dark cycle, in order to synchronise with the external day. Chrono-tailored or circadian drug delivery systems (DDS) aim to optimise drug delivery by releasing drugs at specific times of day to align with circadian rhythms within the body. Although this approach is still relatively new, it has the potential to enhance drug efficacy, minimise side effects, and improve patient compliance. Chrono-tailored DDS have been explored and implemented in various conditions, including asthma, hypertension, and cancer. This review aims to introduce the biology of circadian rhythms and provide an overview of the current research on chrono-tailored DDS, with a particular focus on immunological applications and vaccination. Finally, we draw on some of the key challenges which need to be overcome for chrono-tailored DDS before they can be translated to more widespread use in clinical practice.
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Affiliation(s)
- Christine T Butler
- Curtis Clock Laboratory, School of Pharmacy and Biomolecular Sciences and Tissue Engineering Research Group (TERG), Royal College of Surgeons in Ireland RCSI, Dublin, Ireland
| | - Aoife M Rodgers
- The Wellcome Wolfson Institute for Experimental Medicine, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7B, UK
| | - Annie M Curtis
- Curtis Clock Laboratory, School of Pharmacy and Biomolecular Sciences and Tissue Engineering Research Group (TERG), Royal College of Surgeons in Ireland RCSI, Dublin, Ireland.
| | - Ryan F Donnelly
- School of Pharmacy, Queen's University Belfast, Belfast, BT9 7BL, UK.
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2
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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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3
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Francisco JC, Virshup DM. Hierarchical and scaffolded phosphorylation of two degrons controls PER2 stability. J Biol Chem 2024; 300:107391. [PMID: 38777144 DOI: 10.1016/j.jbc.2024.107391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 04/30/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The duration of the transcription-repression cycles that give rise to mammalian circadian rhythms is largely determined by the stability of the PERIOD (PER) protein, the rate-limiting components of the molecular clock. The degradation of PERs is tightly regulated by multisite phosphorylation by casein kinase 1 (CK1δ/ε). In this phosphoswitch, phosphorylation of a PER2 degron [degron 2 (D2)] causes degradation, while phosphorylation of the PER2 familial advanced sleep phase (FASP) domain blocks CK1 activity on the degron, stabilizing PER2. However, this model and many other studies of PER2 degradation do not include the second degron of PER2 that is conserved in PER1, termed degron 1 (D1). We examined how these two degrons contribute to PER2 stability, affect the balance of the phosphoswitch, and how they are differentiated by CK1. Using PER2-luciferase fusions and real-time luminometry, we investigated the contribution of both D2 and of CK1-PER2 binding. We find that D1, like D2, is a substrate of CK1 but that D1 plays only a 'backup' role in PER2 degradation. Notably, CK1 bound to a PER1:PER2 dimer protein can phosphorylate PER1 D1 in trans. This scaffolded phosphorylation provides additional levels of control to PER stability and circadian rhythms.
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Affiliation(s)
- Joel Celio Francisco
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore; Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA.
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4
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Sharma SA, Oladejo SO, Kuang Z. Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology. Cell Chem Biol 2024:S2451-9456(24)00178-8. [PMID: 38776923 DOI: 10.1016/j.chembiol.2024.04.016] [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: 12/15/2023] [Revised: 03/22/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.
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Affiliation(s)
- Samskrathi Aravinda Sharma
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Sarah Olanrewaju Oladejo
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Zheng Kuang
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
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5
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Chen K, Wang Y, Li D, Wu R, Wang J, Wei W, Zhu W, Xie W, Feng D, He Y. Biological clock regulation by the PER gene family: a new perspective on tumor development. Front Cell Dev Biol 2024; 12:1332506. [PMID: 38813085 PMCID: PMC11133573 DOI: 10.3389/fcell.2024.1332506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024] Open
Abstract
The Period (PER) gene family is one of the core components of the circadian clock, with substantial correlations between the PER genes and cancers identified in extensive researches. Abnormal mutations in PER genes can influence cell function, metabolic activity, immunity, and therapy responses, thereby promoting the initiation and development of cancers. This ultimately results in unequal cancers progression and prognosis in patients. This leads to variable cancer progression and prognosis among patients. In-depth studies on the interactions between the PER genes and cancers can reveal novel strategies for cancer detection and treatment. In this review, we aim to provide a comprehensive overview of the latest research on the role of the PER gene family in cancer.
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Affiliation(s)
- Kai Chen
- Department of Urology, The First Hospital of Jiaxing, The Affiliated Hospital of Jiaxing University, Jia Xing, China
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Yaohui Wang
- Department of Urology, The Third Medical Center of PLA General Hospital, Beijing, China
| | - Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Zhu
- Department of Urology, The First Hospital of Jiaxing, The Affiliated Hospital of Jiaxing University, Jia Xing, China
| | - Wenhua Xie
- Department of Urology, The First Hospital of Jiaxing, The Affiliated Hospital of Jiaxing University, Jia Xing, China
| | - Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
| | - Yi He
- Department of Urology, The First Hospital of Jiaxing, The Affiliated Hospital of Jiaxing University, Jia Xing, China
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6
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Cai YD, Chow GK, Hidalgo S, Liu X, Jackson KC, Vasquez CD, Gao ZY, Lam VH, Tabuloc CA, Zheng H, Zhao C, Chiu JC. Alternative splicing of clock transcript mediates the response of circadian clocks to temperature changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593646. [PMID: 38766142 PMCID: PMC11100826 DOI: 10.1101/2024.05.10.593646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Circadian clocks respond to temperature changes over the calendar year, allowing organisms to adjust their daily biological rhythms to optimize health and fitness. In Drosophila, seasonal adaptations and temperature compensation are regulated by temperature-sensitive alternative splicing (AS) of period (per) and timeless (tim) genes that encode key transcriptional repressors of clock gene expression. Although clock (clk) gene encodes the critical activator of clock gene expression, AS of its transcripts and its potential role in temperature regulation of clock function have not been explored. We therefore sought to investigate whether clk exhibits AS in response to temperature and the functional changes of the differentially spliced transcripts. We observed that clk transcripts indeed undergo temperature-sensitive AS. Specifically, cold temperature leads to the production of an alternative clk transcript, hereinafter termed clk-cold, which encodes a CLK isoform with an in-frame deletion of four amino acids proximal to the DNA binding domain. Notably, serine 13 (S13), which we found to be a CK1α-dependent phosphorylation site, is among the four amino acids deleted in CLK-cold protein. Using a combination of transgenic fly, tissue culture, and in vitro experiments, we demonstrated that upon phosphorylation at CLK(S13), CLK-DNA interaction is reduced, thus decreasing CLK occupancy at clock gene promoters. This is in agreement with our findings that CLK occupancy at clock genes and transcriptional output are elevated at cold temperature, which can be explained by the higher amounts of CLK-cold isoforms that lack S13 residue. This study provides new insights into the complex collaboration between AS and phospho-regulation in shaping temperature responses of the circadian clock.
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Affiliation(s)
- Yao D. Cai
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Gary K. Chow
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Sergio Hidalgo
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Xianhui Liu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Kiya C. Jackson
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Cameron D. Vasquez
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Zita Y. Gao
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Vu H. Lam
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Christine A. Tabuloc
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Caifeng Zhao
- Biological Mass Spectrometry Facility, Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Joanna C. Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California Davis, One Shields Ave, Davis, CA 95616, USA
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7
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Spangler RK, Ashley GE, Braun K, Wruck D, Ramos-Coronado A, Ragle JM, Iesmantavicius V, Hess D, Partch CL, Großhans H, Ward JD. A conserved chronobiological complex times C. elegans development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593322. [PMID: 38766223 PMCID: PMC11100808 DOI: 10.1101/2024.05.09.593322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mammalian PAS-domain protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. However, while the function of PER in animal circadian rhythms is well understood molecularly and mechanistically, this is not true for the function of LIN-42 in timing rhythmic development. Here, using targeted deletions, we find that the LIN-42 PAS domains are dispensable for the protein's function in timing molts. Instead, we observe arrhythmic molts upon deletion of a distinct sequence element, conserved with PER. We show that this element mediates stable binding to KIN-20, the C. elegans CK1δ/ε orthologue. We demonstrate that CK1δ phosphorylates LIN-42 and define two conserved helical motifs, CK1δ-binding domain A (CK1BD-A) and CK1BD-B, that have distinct roles in controlling CK1δ-binding and kinase activity in vitro. KIN-20 and the LIN-42 CK1BD are required for proper molting timing in vivo. These interactions mirror the central role of a stable circadian PER-CK1 complex in setting a robust ~24-hour period. Hence, our results establish LIN-42/PER - KIN-20/CK1δ/ε as a functionally conserved signaling module of two distinct chronobiological systems.
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Affiliation(s)
- Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Daniel Wruck
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea Ramos-Coronado
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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8
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Del Olmo M, Legewie S, Brunner M, Höfer T, Kramer A, Blüthgen N, Herzel H. Network switches and their role in circadian clocks. J Biol Chem 2024; 300:107220. [PMID: 38522517 PMCID: PMC11044057 DOI: 10.1016/j.jbc.2024.107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Circadian rhythms are generated by complex interactions among genes and proteins. Self-sustained ∼24 h oscillations require negative feedback loops and sufficiently strong nonlinearities that are the product of molecular and network switches. Here, we review common mechanisms to obtain switch-like behavior, including cooperativity, antagonistic enzymes, multisite phosphorylation, positive feedback, and sequestration. We discuss how network switches play a crucial role as essential components in cellular circadian clocks, serving as integral parts of transcription-translation feedback loops that form the basis of circadian rhythm generation. The design principles of network switches and circadian clocks are illustrated by representative mathematical models that include bistable systems and negative feedback loops combined with Hill functions. This work underscores the importance of negative feedback loops and network switches as essential design principles for biological oscillations, emphasizing how an understanding of theoretical concepts can provide insights into the mechanisms generating biological rhythms.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Michael Brunner
- Biochemistry Center, Universität Heidelberg, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Universität Heidelberg, Heidelberg, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
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9
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Sun L, Huang K, Deng Q, Zhu Y, Cao Y, Dong K, Yang S, Li Y, Wu S, Huang R. REV-ERBα negatively regulates NLRP6 transcription and reduces the severity of Salmonella infection in mice. Heliyon 2024; 10:e28432. [PMID: 38628724 PMCID: PMC11019167 DOI: 10.1016/j.heliyon.2024.e28432] [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: 11/10/2023] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Non-typhoidal Salmonella infection is among the most frequent foodborne diseases threatening human health worldwide. The host circadian clock orchestrates daily rhythms to adapt to environmental changes, including coordinating immune function in response to potential infections. However, the molecular mechanisms underlying the interplay between the circadian clock and the immune system in modulating infection processes are incompletely understood. Here, we demonstrate that NLRP6, a novel nucleotide-oligomerization domain (NOD)-like receptor (NLR) family member highly expressed in the intestine, is closely associated with the differential day-night response to Salmonella infection. The core clock component REV-ERBα negatively regulates NLRP6 transcription, leading to the rhythmic expression of NLRP6 and the secretion of IL-18 in intestinal epithelial cells, playing a crucial role in mediating the differential day-night response to Salmonella infection. Activating REV-ERBα with agonist SR9009 in wild-type mice attenuated the severity of infection by decreasing the NLRP6 level in intestinal epithelial cells. Our findings provide new insights into the association between the host circadian clock and the immune response to enteric infections by revealing the regulation of Salmonella infection via the inhibitory effect of REV-ERBα on NLRP6 transcription. Targeting REV-ERBα to modulate NLRP6 activation may be a potential therapeutic strategy for bacterial infections.
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Affiliation(s)
- Lanqing Sun
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
- Department of Laboratory Medicine, Affiliated Hospital of Jiangnan University, Wuxi, 214000 Jiangsu, PR China
| | - Kai Huang
- Orthopaedic Institute, Wuxi 9th People's Hospital Affiliated to Soochow University, Wuxi, 214062 Jiangsu, PR China
- Cambridge–Suda Genomic Resource Center, Jiangsu Key Laboratory of Neuropsychiatric Diseases, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
| | - Qifeng Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 Guangdong, PR China
| | - Yuan Zhu
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
- Department of Laboratory Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, 315010 Zhejiang, PR China
| | - Yu Cao
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
- Laboratory Department, Children's Hospital of Soochow University, Suzhou, 215025 Jiangsu, PR China
| | - Kedi Dong
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
- Department of Blood Transfusion, The First Affiliated Hospital of Ningbo University, Ningbo, 315010 Zhejiang, PR China
| | - Sidi Yang
- Guangzhou National Laboratory, Guangzhou International BioIsland, Guangzhou, 510005 Guangdong, PR China
| | - Yuanyuan Li
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
| | - Shuyan Wu
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
| | - Rui Huang
- Department of Medical Microbiology, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, 215123 Jiangsu, PR China
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10
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McCarver S, Hanna L, Samant A, Thompson AA, Seierstad M, Saha A, Wu D, Lord B, Sutton SW, Shah V, Milligan CM, Wennerholm M, Shelton J, Lebold TP, Shireman BT. Structure-Based Optimization of Selective and Brain Penetrant CK1δ Inhibitors for the Treatment of Circadian Disruptions. ACS Med Chem Lett 2024; 15:486-492. [PMID: 38628796 PMCID: PMC11017389 DOI: 10.1021/acsmedchemlett.3c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Neuropsychiatric disorders such as major depressive disorders and schizophrenia are often associated with disruptions to the normal 24 h sleep wake cycle. Casein kinase 1 (CK1δ) is an integral part of the molecular machinery that regulates circadian rhythms. Starting from a cluster of bicyclic pyrazoles identified from a virtual screening effort, we utilized structure-based drug design to identify and reinforce a unique "hinge-flip" binding mode that provides a high degree of selectivity for CK1δ versus the kinome. Pharmacokinetics, brain exposure, and target engagement as measured by ex vivo autoradiography are described for advanced analogs.
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Affiliation(s)
- Stefan McCarver
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | | | | | - Aaron A. Thompson
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Mark Seierstad
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Arjun Saha
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Dongpei Wu
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Brian Lord
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Steven W. Sutton
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Vishal Shah
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Cynthia M. Milligan
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Michelle Wennerholm
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Jonathan Shelton
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Terry P. Lebold
- Janssen Research and Development, San Diego, California 92121-1126, United
States
| | - Brock T. Shireman
- Janssen Research and Development, San Diego, California 92121-1126, United
States
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11
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Zhou Q, Wang R, Su Y, Wang B, Zhang Y, Qin X. The molecular circadian rhythms regulating the cell cycle. J Cell Biochem 2024; 125:e30539. [PMID: 38372014 DOI: 10.1002/jcb.30539] [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: 10/18/2023] [Revised: 01/25/2024] [Accepted: 02/02/2024] [Indexed: 02/20/2024]
Abstract
The circadian clock controls the expression of a large proportion of protein-coding genes in mammals and can modulate a wide range of physiological processes. Recent studies have demonstrated that disruption or dysregulation of the circadian clock is involved in the development and progression of several diseases, including cancer. The cell cycle is considered to be the fundamental process related to cancer. Accumulating evidence suggests that the circadian clock can control the expression of a large number of genes related to the cell cycle. This article reviews the mechanism of cell cycle-related genes whose chromatin regulatory elements are rhythmically occupied by core circadian clock transcription factors, while their RNAs are rhythmically expressed. This article further reviews the identified oscillatory cell cycle-related genes in higher organisms such as baboons and humans. The potential functions of these identified genes in regulating cell cycle progression are also discussed. Understanding how the molecular clock controls the expression of cell cycle genes will be beneficial for combating and treating cancer.
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Affiliation(s)
- Qin Zhou
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Ruohan Wang
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Yunxia Su
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Bowen Wang
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Yunfei Zhang
- Modern Experiment Technology Center, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
| | - Ximing Qin
- Institute of Health Sciences and Technology, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui Province, China
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12
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Jeong EM, Kim JK. A robust ultrasensitive transcriptional switch in noisy cellular environments. NPJ Syst Biol Appl 2024; 10:30. [PMID: 38493227 PMCID: PMC10944533 DOI: 10.1038/s41540-024-00356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Ultrasensitive transcriptional switches enable sharp transitions between transcriptional on and off states and are essential for cells to respond to environmental cues with high fidelity. However, conventional switches, which rely on direct repressor-DNA binding, are extremely noise-sensitive, leading to unintended changes in gene expression. Here, through model simulations and analysis, we discovered that an alternative design combining three indirect transcriptional repression mechanisms, sequestration, blocking, and displacement, can generate a noise-resilient ultrasensitive switch. Although sequestration alone can generate an ultrasensitive switch, it remains sensitive to noise because the unintended transcriptional state induced by noise persists for long periods. However, by jointly utilizing blocking and displacement, these noise-induced transitions can be rapidly restored to the original transcriptional state. Because this transcriptional switch is effective in noisy cellular contexts, it goes beyond previous synthetic transcriptional switches, making it particularly valuable for robust synthetic system design. Our findings also provide insights into the evolution of robust ultrasensitive switches in cells. Specifically, the concurrent use of seemingly redundant indirect repression mechanisms in diverse biological systems appears to be a strategy to achieve noise-resilience of ultrasensitive switches.
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Affiliation(s)
- Eui Min Jeong
- Biomedical Mathematics Group, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jae Kyoung Kim
- Biomedical Mathematics Group, Institute for Basic Science, 55, Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea.
- Department of Mathematical Sciences, KAIST, 291, Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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13
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Liu XL, Duan Z, Yu M, Liu X. Epigenetic control of circadian clocks by environmental signals. Trends Cell Biol 2024:S0962-8924(24)00028-X. [PMID: 38423855 DOI: 10.1016/j.tcb.2024.02.005] [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: 12/14/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024]
Abstract
Circadian clocks have evolved to enable organisms to respond to daily environmental changes. Maintaining a robust circadian rhythm under various perturbations and stresses is essential for the fitness of an organism. In the core circadian oscillator conserved in eukaryotes (from fungi to mammals), a negative feedback loop based on both transcription and translation drives circadian rhythms. The expression of circadian clock genes depends both on the binding of transcription activators at the promoter and on the chromatin state of the clock genes, and epigenetic modifications of chromatin are crucial for transcriptional regulation of circadian clock genes. Herein we review current knowledge of epigenetic regulation of circadian clock mechanisms and discuss how environmental cues can control clock gene expression by affecting chromatin states.
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Affiliation(s)
- Xiao-Lan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeyu Duan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muqun Yu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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14
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Yang Y, Wu G, Sancar A, Hogenesch JB. Mutations of the circadian clock genes Cry, Per, or Bmal1 have different effects on the transcribed and nontranscribed strands of cycling genes. Proc Natl Acad Sci U S A 2024; 121:e2316731121. [PMID: 38359290 PMCID: PMC10895256 DOI: 10.1073/pnas.2316731121] [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: 09/26/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
One important goal of circadian medicine is to apply time-of-day dosing to improve the efficacy of chemotherapy. However, limited knowledge of how the circadian clock regulates DNA repair presents a challenge to mechanism-based clinical application. We studied time-series genome-wide nucleotide excision repair in liver and kidney of wild type and three different clock mutant genotypes (Cry1-/-Cry2-/-, Per1-/-Per2-/-, and Bmal1-/-). Rhythmic repair on the nontranscribed strand was lost in all three clock mutants. Conversely, rhythmic repair of hundreds of genes on the transcribed strand (TSs) persisted in the livers of Cry1-/-Cry2-/- and Per1-/-Per2-/- mice. We identified a tissue-specific, promoter element-driven repair mode on TSs of collagen and angiogenesis genes in the absence of clock activators or repressors. Furthermore, repair on TSs of thousands of genes was altered when the circadian clock is disrupted. These data contribute to a better understanding of the regulatory role of the circadian clock on nucleotide excision repair in mammals and may be invaluable toward the design of time-aware platinum-based interventions in cancer.
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Affiliation(s)
- Yanyan Yang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Gang Wu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - John B Hogenesch
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45267
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Divisions of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
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15
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Song YM, Campbell S, Shiau L, Kim JK, Ott W. Noisy Delay Denoises Biochemical Oscillators. PHYSICAL REVIEW LETTERS 2024; 132:078402. [PMID: 38427894 DOI: 10.1103/physrevlett.132.078402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/17/2023] [Indexed: 03/03/2024]
Abstract
Genetic oscillations are generated by delayed transcriptional negative feedback loops, wherein repressor proteins inhibit their own synthesis after a temporal production delay. This delay is distributed because it arises from a sequence of noisy processes, including transcription, translocation, translation, and folding. Because the delay determines repression timing and, therefore, oscillation period, it has been commonly believed that delay noise weakens oscillatory dynamics. Here, we demonstrate that noisy delay can surprisingly denoise genetic oscillators. Specifically, moderate delay noise improves the signal-to-noise ratio and sharpens oscillation peaks, all without impacting period and amplitude. We show that this denoising phenomenon occurs in a variety of well-studied genetic oscillators, and we use queueing theory to uncover the universal mechanisms that produce it.
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Affiliation(s)
- Yun Min Song
- Department of Mathematical Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Sean Campbell
- Department of Mathematics, University of Houston, Houston, Texas 77204, USA
| | - LieJune Shiau
- Department of Mathematics and Statistics, University of Houston Clear Lake, Houston, Texas 77058, USA
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, KAIST, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Pioneer Research Center for Mathematical and Computational Sciences, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - William Ott
- Department of Mathematics, University of Houston, Houston, Texas 77204, USA
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16
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Rojas BL, Vazquez-Rivera E, Partch CL, Bradfield CA. Dimerization Rules of Mammalian PAS Proteins. J Mol Biol 2024; 436:168406. [PMID: 38109992 PMCID: PMC10922841 DOI: 10.1016/j.jmb.2023.168406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 12/20/2023]
Abstract
The PAS (PER, ARNT, SIM) protein family plays a vital role in mammalian biology and human disease. This analysis arose from an interest in the signaling mechanics by the Ah receptor (AHR) and the Ah receptor nuclear translocator (ARNT). After more than fifty years by studying this and related mammalian sensor systems, describing the role of PAS domains in signal transduction is still challenging. In this perspective, we attempt to interpret recent studies of mammalian PAS protein structure and consider how this new insight might explain how these domains are employed in human signal transduction with an eye towards developing strategies to target and engineer these molecules for a new generation of therapeutics. Our approach is to integrate our understanding of PAS protein history, cell biology, and molecular biology with recent structural discoveries to help explain the mechanics of mammalian PAS protein signaling. As a learning set, we focus on sequences and crystal structures of mammalian PAS protein dimers that can be visualized using readily available software.
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Affiliation(s)
- Brenda L Rojas
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA
| | | | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California at Santa Cruz, USA
| | - Christopher A Bradfield
- Molecular and Environmental Toxicology Center, University of Wisconsin at Madison, USA; McArdle Laboratory for Cancer Research. University of Wisconsin, School of Medicine and Public Health, Madison, WI, USA.
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17
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Sharma D, Partch CL. PAS Dimerization at the Nexus of the Mammalian Circadian Clock. J Mol Biol 2024; 436:168341. [PMID: 37924861 DOI: 10.1016/j.jmb.2023.168341] [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: 07/17/2023] [Revised: 10/23/2023] [Accepted: 10/29/2023] [Indexed: 11/06/2023]
Abstract
Circadian rhythms are genetically encoded molecular clocks for internal biological timekeeping. Organisms from single-cell bacteria to humans use these clocks to adapt to the external environment and synchronize their physiology and behavior to solar light/dark cycles. Although the proteins that constitute the molecular 'cogs' and give rise to circadian rhythms are now known, we still lack a detailed understanding of how these proteins interact to generate and sustain the ∼24-hour circadian clock. Structural studies have helped to expand the architecture of clock proteins and have revealed the abundance of the only well-defined structured regions in the mammalian clock called Per-ARNT-Sim (PAS) domains. PAS domains are modular, evolutionarily conserved sensory and signaling domains that typically mediate protein-protein interactions. In the mammalian circadian clock, PAS domains modulate homo and heterodimerization of several core clock proteins that assemble into transcription factors or repressors. This review will focus on the functional importance of the PAS domains in the circadian clock from a biophysical and biochemical standpoint and describe their roles in clock protein interactions and circadian timekeeping.
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Affiliation(s)
- Diksha Sharma
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California Santa Cruz, CA, United States; Center for Circadian Biology, University of California San Diego, CA, United States.
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18
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Chiou YY, Lee CY, Yang HW, Cheng WC, Ji KD. Circadian modulation of glucose utilization via CRY1-mediated repression of Pdk1 expression. J Biol Chem 2024; 300:105637. [PMID: 38199564 PMCID: PMC10869264 DOI: 10.1016/j.jbc.2024.105637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
Life adapts to daily environmental changes through circadian rhythms, exhibiting spontaneous oscillations of biological processes. These daily functional oscillations must match the metabolic requirements responding to the time of the day. We focus on the molecular mechanism of how the circadian clock regulates glucose, the primary resource for energy production and other biosynthetic pathways. The complex regulation of the circadian rhythm includes many proteins that control this process at the transcriptional and translational levels and by protein-protein interactions. We have investigated the action of one of these proteins, cryptochrome (CRY), whose elevated mRNA and protein levels repress the function of an activator in the transcription-translation feedback loop, and this activator causes elevated Cry1 mRNA. We used a genome-edited cell line model to investigate downstream genes affected explicitly by the repressor CRY. We found that CRY can repress glycolytic genes, particularly that of the gatekeeper, pyruvate dehydrogenase kinase 1 (Pdk1), decreasing lactate accumulation and glucose utilization. CRY1-mediated decrease of Pdk1 expression can also be observed in a breast cancer cell line MDA-MB-231, whose glycolysis is associated with Pdk1 expression. We also found that exogenous expression of CRY1 in the MDA-MB-231 decreases glucose usage and growth rate. Furthermore, reduced CRY1 levels and the increased phosphorylation of PDK1 substrate were observed when cells were grown in suspension compared to cells grown in adhesion. Our data supports a model that the transcription-translation feedback loop can regulate the glucose metabolic pathway through Pdk1 gene expression according to the time of the day.
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Affiliation(s)
- Yi-Ying Chiou
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
| | - Cing-Yun Lee
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Hao-Wei Yang
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wei-Cheng Cheng
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kun-Da Ji
- Graduate Institute of Biochemistry, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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19
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Lai H, Xiang X, Long X, Chen Z, Liu Y, Huang X. Multi-omics and single-cell sequencing analyses reveal the potential significance of circadian pathways in cancer therapy. Expert Rev Mol Diagn 2024; 24:107-121. [PMID: 38288973 DOI: 10.1080/14737159.2023.2296668] [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: 05/17/2023] [Accepted: 11/24/2023] [Indexed: 02/22/2024]
Abstract
BACKGROUND Circadian rhythm disturbance is an independent risk factor for cancer. However, few studies have been reported on circadian rhythm related genes (CRGs) in cancer, so it is important to further explore the impact of CRGs in pan-cancer. RESEARCH DESIGN AND METHODS The Cancer Genome Atlas database was used to collect cancer-related data such as copy number variation, single nucleotide variants, methylation, and survival differences. Immunohistochemistry (IHC) was used to verify the expression of circadian rhythm hub genes. The circadian pathway scores (CRS) were calculated using single-sample gene enrichment analysis. TIMER and GEPIA databases were used for immune-cell integration and assessment. Single-cell sequencing data was used to evaluate the abundance of CRS in tumor microenvironment cells. RESULTS In this study, we found that the expression of circadian pathway varies between tumors. CSNK1E was significantly up-regulated in most tumors and CRY2 was significantly down-regulated in most tumors. The protein interaction network suggested CRY2 as the core gene and IHC verified its significant low expression in KIRC. In addition, CRGs were found to be protective factors in most tumors and have the potential to act as specific immune markers in different tumors. CRS was significantly lower in abundance in most tumors. CRS was significantly associated with overall survival in tumor patients and associated with the expression of many immune cells in the tumor immune microenvironment. CRS is significantly associated with tumor mutational burden and microsatellite instability scores in most tumors and may serve as a potential immunotherapeutic marker. CONCLUSIONS The circadian rhythm pathway may be a breakthrough point in regulating the tumor microenvironment meanwhile a suitable immunotherapy method in the future.
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Affiliation(s)
- Hao Lai
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Xiaoyun Xiang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Xingqing Long
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Zuyuan Chen
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Yanling Liu
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
| | - Xiaoliang Huang
- Division of Colorectal & Anal Surgery, Department of Gastrointestinal Surgery, Guangxi Medical University Cancer Hospital, Nanning, The People's Republic of China
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20
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Xie P, Xie X, Ye C, Dean KM, Laothamatas I, Taufique SKT, Takahashi J, Yamazaki S, Xu Y, Liu Y. Mammalian circadian clock proteins form dynamic interacting microbodies distinct from phase separation. Proc Natl Acad Sci U S A 2023; 120:e2318274120. [PMID: 38127982 PMCID: PMC10756265 DOI: 10.1073/pnas.2318274120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) underlies diverse biological processes. Because most LLPS studies were performed in vitro using recombinant proteins or in cells that overexpress protein, the physiological relevance of LLPS for endogenous protein is often unclear. PERIOD, the intrinsically disordered domain-rich proteins, are central mammalian circadian clock components and interact with other clock proteins in the core circadian negative feedback loop. Different core clock proteins were previously shown to form large complexes. Circadian clock studies often rely on experiments that overexpress clock proteins. Here, we show that when Per2 transgene was stably expressed in cells, PER2 protein formed nuclear phosphorylation-dependent slow-moving LLPS condensates that recruited other clock proteins. Super-resolution microscopy of endogenous PER2, however, revealed formation of circadian-controlled, rapidly diffusing nuclear microbodies that were resistant to protein concentration changes, hexanediol treatment, and loss of phosphorylation, indicating that they are distinct from the LLPS condensates caused by protein overexpression. Surprisingly, only a small fraction of endogenous PER2 microbodies transiently interact with endogenous BMAL1 and CRY1, a conclusion that was confirmed in cells and in mice tissues, suggesting an enzyme-like mechanism in the circadian negative feedback process. Together, these results demonstrate that the dynamic interactions of core clock proteins are a key feature of mammalian circadian clock mechanism and the importance of examining endogenous proteins in LLPS and circadian clock studies.
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Affiliation(s)
- Pancheng Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu215123, China
| | - Xiaowen Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Congrong Ye
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics and Cecil H. and Ida Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - Isara Laothamatas
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - S. K. Tahajjul Taufique
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - Joseph Takahashi
- HHMI, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - Shin Yamazaki
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX75390-9111
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX75390
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21
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Gao Y, Xu H, Jia B, Liu Y, Hassan A, Huang Q. Circadian Rhythms of Locomotor Activity Mediated by Cryptochrome 2 and Period 1 Genes in the Termites Reticulitermes chinensis and Odontotermes formosanus. INSECTS 2023; 15:1. [PMID: 38276815 PMCID: PMC10816429 DOI: 10.3390/insects15010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024]
Abstract
Locomotor activity rhythms are crucial for foraging, mating and predator avoidance in insects. Although the circadian rhythms of activity have been studied in several termite species, the molecular mechanisms of circadian rhythms in termites are still unclear. In this study, we found that two termite species, R. chinensis and O. formosanus, exhibited clear circadian rhythms of locomotor activity in constant darkness along with rhythmically expressed core clock genes, Cry2 and Per1. The knockdown of Cry2 or Per1 expression in the two termite species disrupted the circadian rhythms of locomotor activity and markedly reduced locomotor activity in constant darkness, which demonstrates that Cry2 and Per1 can mediate the circadian rhythms of locomotor activity in termites in constant darkness. We suggest that locomotor activity in subterranean termites is controlled by the circadian clock.
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Affiliation(s)
- Yongyong Gao
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (H.X.); (B.J.); (Y.L.); (A.H.)
- Research and Development Centre of Ecological and Sustainable Application of Microbial Industry of the Loess Plateau in Shaanxi Province, College of Life Science, Yan’an University, Yan’an 716000, China
- Key Laboratory of Termite Control of Ministry of Water Resources, Huazhong Agricultural University, Wuhan 430070, China
| | - Huan Xu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (H.X.); (B.J.); (Y.L.); (A.H.)
- Research and Development Centre of Ecological and Sustainable Application of Microbial Industry of the Loess Plateau in Shaanxi Province, College of Life Science, Yan’an University, Yan’an 716000, China
- Key Laboratory of Termite Control of Ministry of Water Resources, Huazhong Agricultural University, Wuhan 430070, China
| | - Bao Jia
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (H.X.); (B.J.); (Y.L.); (A.H.)
| | - Yutong Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (H.X.); (B.J.); (Y.L.); (A.H.)
| | - Ali Hassan
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (H.X.); (B.J.); (Y.L.); (A.H.)
| | - Qiuying Huang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.G.); (H.X.); (B.J.); (Y.L.); (A.H.)
- Key Laboratory of Termite Control of Ministry of Water Resources, Huazhong Agricultural University, Wuhan 430070, China
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22
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Ventresca C, Mohamed W, Russel WA, Ay A, Ingram KK. Machine learning analyses reveal circadian clock features predictive of anxiety among UK biobank participants. Sci Rep 2023; 13:22304. [PMID: 38102312 PMCID: PMC10724169 DOI: 10.1038/s41598-023-49644-7] [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: 07/16/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
Mood disorders, including depression and anxiety, affect almost one-fifth of the world's adult population and are becoming increasingly prevalent. Mutations in circadian clock genes have previously been associated with mood disorders both directly and indirectly through alterations in circadian phase, suggesting that the circadian clock influences multiple molecular pathways involved in mood. By targeting previously identified single nucleotide polymorphisms (SNPs) that have been implicated in anxiety and depressive disorders, we use a combination of statistical and machine learning techniques to investigate associations with the generalized anxiety disorder assessment (GAD-7) scores in a UK Biobank sample of 90,882 individuals. As in previous studies, we observed that females exhibited higher GAD-7 scores than males regardless of genotype. Interestingly, we found no significant effects on anxiety from individual circadian gene variants; only circadian genotypes with multiple SNP variants showed significant associations with anxiety. For both sexes, severe anxiety is associated with a 120-fold increase in odds for individuals with CRY2_AG(rs1083852)/ZBTB20_TT(rs1394593) genotypes and is associated with a near 40-fold reduction in odds for individuals with PER3-A_CG(rs228697)/ZBTB20_TT(rs1394593) genotypes. We also report several sex-specific associations with anxiety. In females, the CRY2/ZBTB20 genotype combination showed a > 200-fold increase in odds of anxiety and PER3/ZBTB20 and CRY1 /PER3-A genotype combinations also appeared as female risk factors. In males, CRY1/PER3-A and PER3-B/ZBTB20 genotype combinations were associated with anxiety risk. Mediation analysis revealed direct associations of CRY2/ZBTB20 variant genotypes with moderate anxiety in females and CRY1/PER3-A variant genotypes with severe anxiety in males. The association of CRY1/PER3-A variant genotypes with severe anxiety in females was partially mediated by extreme evening chronotype. Our results reinforce existing findings that females exhibit stronger anxiety outcomes than males, and provide evidence for circadian gene associations with anxiety, particularly in females. Our analyses only identified significant associations using two-gene combinations, underscoring the importance of combined gene effects on anxiety risk. We describe novel, robust associations between gene combinations involving the ZBTB20 SNP (rs1394593) and risk of anxiety symptoms in a large population sample. Our findings also support previous findings that the ZBTB20 SNP is an important factor in mood disorders, including seasonal affective disorder. Our results suggest that reduced expression of this gene significantly modulates the risk of anxiety symptoms through direct influences on mood-related pathways. Together, these observations provide novel links between the circadian clockwork and anxiety symptoms and identify potential molecular pathways through which clock genes may influence anxiety risk.
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Affiliation(s)
- Cole Ventresca
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Department of Computer Science, Colgate University, Hamilton, NY, USA
| | - Wael Mohamed
- Department of Computer Science, Colgate University, Hamilton, NY, USA
- Department of Psychological and Brain Sciences, Colgate University, Hamilton, NY, USA
| | | | - Ahmet Ay
- Department of Mathematics, Colgate University, Hamilton, NY, USA
- Department of Biology, Colgate University, Hamilton, NY, USA
| | - Krista K Ingram
- Department of Biology, Colgate University, Hamilton, NY, USA.
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23
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Parlak GC, Baris I, Gul S, Kavakli IH. Functional characterization of the CRY2 circadian clock component variant p.Ser420Phe revealed a new degradation pathway for CRY2. J Biol Chem 2023; 299:105451. [PMID: 37951306 PMCID: PMC10731238 DOI: 10.1016/j.jbc.2023.105451] [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: 09/14/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/13/2023] Open
Abstract
Cryptochromes (CRYs) are essential components of the circadian clock, playing a pivotal role as transcriptional repressors. Despite their significance, the precise mechanisms underlying CRYs' involvement in the circadian clock remain incompletely understood. In this study, we identified a rare CRY2 variant, p.Ser420Phe, from the 1000 Genomes Project and Ensembl database that is located in the functionally important coiled-coil-like helix (CC-helix) region. Functional characterization of this variant at the cellular level revealed that p.Ser420Phe CRY2 had reduced repression activity on CLOCK:BMAL1-driven transcription due to its reduced affinity to the core clock protein PER2 and defective translocation into the nucleus. Intriguingly, the CRY2 variant exhibited an unexpected resistance to degradation via the canonical proteasomal pathway, primarily due to the loss of interactions with E3 ligases (FBXL3 and FBXL21), which suggests Ser-420 of CRY2 is required for the interaction with E3 ligases. Further studies revealed that wild-type and CRY2 variants are degraded by the lysosomal-mediated degradation pathway, a mechanism not previously associated with CRY2. Surprisingly, our complementation study with Cry1-/-Cry2-/- double knockout mouse embryonic fibroblast cells indicated that the CRY2 variant caused a 7 h shorter circadian period length in contrast to the observed prolonged period length in CRY2-/- cell lines. In summary, this study reveals a hitherto unknown degradation pathway for CRY2, shedding new light on the regulation of circadian rhythm period length.
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Affiliation(s)
- Gizem Cagla Parlak
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkiye
| | - Ibrahim Baris
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkiye
| | - Seref Gul
- Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Turkiye
| | - Ibrahim Halil Kavakli
- Department of Molecular Biology and Genetics, Koc University, Istanbul, Turkiye; Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkiye.
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24
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Xie P, Xie X, Ye C, Dean KM, Laothamatas I, Taufique SKT, Takahashi J, Yamazaki S, Xu Y, Liu Y. Mammalian circadian clock proteins form dynamic interacting microbodies distinct from phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563153. [PMID: 37961341 PMCID: PMC10634710 DOI: 10.1101/2023.10.19.563153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Liquid-liquid phase separation (LLPS) underlies diverse biological processes. Because most LLPS studies were performed in vitro or in cells that overexpress protein, the physiological relevance of LLPS is unclear. PERIOD proteins are central mammalian circadian clock components and interact with other clock proteins in the core circadian negative feedback loop. Different core clock proteins were previously shown to form large complexes. Here we show that when transgene was stably expressed, PER2 formed nuclear phosphorylation-dependent LLPS condensates that recruited other clock proteins. Super-resolution microscopy of endogenous PER2, however, revealed formation of circadian-controlled, rapidly diffusing microbodies that were resistant to protein concentration changes, hexanediol treatment, and loss of phosphorylation, indicating that they are distinct from the LLPS condensates caused by overexpression. Surprisingly, only a small fraction of endogenous PER2 microbodies transiently interact with endogenous BMAL1 and CRY1, a conclusion that was confirmed in cells and in mice tissues, suggesting an enzyme-like mechanism in the circadian negative feedback process. Together, these results demonstrate that the dynamic interactions of core clock proteins is a key feature of mammalian circadian clock mechanism and the importance of examining endogenous proteins in LLPS and circadian studies.
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Affiliation(s)
- Pancheng Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Cambridge-Su Genomic Resource Center, Soochow University; Suzhou, Jiangsu 215123, China
| | - Xiaowen Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Congrong Ye
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin M. Dean
- Lyda Hill Department of Bioinformatics and Cecil H. and Ida Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Isara Laothamatas
- Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - S K Tahajjul Taufique
- Department of Neuroscience and Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - Joseph Takahashi
- Department of Neuroscience and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - Shin Yamazaki
- Department of Neuroscience and Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390-9111, USA
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University; Suzhou, Jiangsu 215123, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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25
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Yang Y, Abdo AN, Kawara H, Selby CP, Sancar A. Preservation of circadian rhythm in hepatocellular cancer. J Biol Chem 2023; 299:105251. [PMID: 37714462 PMCID: PMC10582759 DOI: 10.1016/j.jbc.2023.105251] [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: 06/16/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023] Open
Abstract
Circadian rhythms are controlled at the cellular level by a molecular clock consisting of several genes/proteins engaged in a transcription-translation-degradation feedback loop. These core clock proteins regulate thousands of tissue-specific genes. Regarding circadian control in neoplastic tissues, reports to date have demonstrated anomalous circadian function in tumor models and cultured tumor cells. We have extended these studies by analyzing circadian rhythmicity genome-wide in a mouse model of liver cancer, in which mice treated with diethylnitrosamine at 15 days develop liver tumors by 6 months. We injected tumor-bearing and control tumor-free mice with cisplatin every 2 h over a 24-h cycle; 2 h after each injection mice were sacrificed and gene expression was measured by XR-Seq (excision repair sequencing) assay. Rhythmic expression of several core clock genes was observed in both healthy liver and tumor, with clock genes in tumor exhibiting typically robust amplitudes and a modest phase advance. Interestingly, although normal hepatic cells and hepatoma cancer cells expressed a comparable number of genes with circadian rhythmicity (clock-controlled genes), there was only about 10% overlap between the rhythmic genes in normal and cancerous cells. "Rhythmic in tumor only" genes exhibited peak expression times mainly in daytime hours, in contrast to the more common pre-dawn and pre-dusk expression times seen in healthy livers. Differential expression of genes in tumors and healthy livers across time may present an opportunity for more efficient anticancer drug treatment as a function of treatment time.
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Affiliation(s)
- Yanyan Yang
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ashraf N Abdo
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Hiroaki Kawara
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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26
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Wilantri S, Grasshoff H, Lange T, Gaber T, Besedovsky L, Buttgereit F. Detecting and exploiting the circadian clock in rheumatoid arthritis. Acta Physiol (Oxf) 2023; 239:e14028. [PMID: 37609862 DOI: 10.1111/apha.14028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/24/2023]
Abstract
Over the past four decades, research on 24-h rhythms has yielded numerous remarkable findings, revealing their genetic, molecular, and physiological significance for immunity and various diseases. Thus, circadian rhythms are of fundamental importance to mammals, as their disruption and misalignment have been associated with many diseases and the abnormal functioning of many physiological processes. In this article, we provide a brief overview of the molecular regulation of 24-h rhythms, their importance for immunity, the deleterious effects of misalignment, the link between such pathological rhythms and rheumatoid arthritis (RA), and the potential exploitation of chronobiological rhythms for the chronotherapy of inflammatory autoimmune diseases, using RA as an example.
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Affiliation(s)
- Siska Wilantri
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), Institute of the Leibniz Association, Berlin, Germany
| | - Hanna Grasshoff
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Tanja Lange
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
- Center of Brain, Behavior and Metabolism (CBBM), University of Lübeck, Lübeck, Germany
| | - Timo Gaber
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), Institute of the Leibniz Association, Berlin, Germany
| | | | - Frank Buttgereit
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), Institute of the Leibniz Association, Berlin, Germany
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27
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Laothamatas I, Rasmussen ES, Green CB, Takahashi JS. Metabolic and chemical architecture of the mammalian circadian clock. Cell Chem Biol 2023; 30:1033-1052. [PMID: 37708890 PMCID: PMC10631358 DOI: 10.1016/j.chembiol.2023.08.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythms are endogenous periodic biological processes that occur on a daily timescale. These rhythms are generated by a transcriptional/translational feedback loop that consists of the CLOCK-BMAL1 heterodimeric transcriptional activator complex and the PER1/2-CRY1/2-CK1δ/ε repressive complex. The output pathways of this molecular feedback loop generate circadian rhythmicity in various biological processes. Among these, metabolism is a primary regulatory target of the circadian clock which can also feedback to modulate clock function. This intertwined relationship between circadian rhythms and metabolism makes circadian clock components promising therapeutic targets. Despite this, pharmacological therapeutics that target the circadian clock are relatively rare. In this review, we hope to stimulate interest in chemical chronobiology by providing a comprehensive background on the molecular mechanism of mammalian circadian rhythms and their connection to metabolism, highlighting important studies in the chemical approach to circadian research, and offering our perspectives on future developments in the field.
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Affiliation(s)
- Isara Laothamatas
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Emil Sjulstok Rasmussen
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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28
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Zhang J, Qiu Z, Zhang Y, Wang G, Hao H. Intracellular spatiotemporal metabolism in connection to target engagement. Adv Drug Deliv Rev 2023; 200:115024. [PMID: 37516411 DOI: 10.1016/j.addr.2023.115024] [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: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
The metabolism in eukaryotic cells is a highly ordered system involving various cellular compartments, which fluctuates based on physiological rhythms. Organelles, as the smallest independent sub-cell unit, are important contributors to cell metabolism and drug metabolism, collectively designated intracellular metabolism. However, disruption of intracellular spatiotemporal metabolism can lead to disease development and progression, as well as drug treatment interference. In this review, we systematically discuss spatiotemporal metabolism in cells and cell subpopulations. In particular, we focused on metabolism compartmentalization and physiological rhythms, including the variation and regulation of metabolic enzymes, metabolic pathways, and metabolites. Additionally, the intricate relationship among intracellular spatiotemporal metabolism, metabolism-related diseases, and drug therapy/toxicity has been discussed. Finally, approaches and strategies for intracellular spatiotemporal metabolism analysis and potential target identification are introduced, along with examples of potential new drug design based on this.
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Affiliation(s)
- Jingwei Zhang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism & Pharmacokinetics, China Pharmaceutical University, Nanjing, China
| | - Zhixia Qiu
- Center of Drug Metabolism and Pharmacokinetics, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yongjie Zhang
- Clinical Pharmacokinetics Laboratory, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Guangji Wang
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism & Pharmacokinetics, China Pharmaceutical University, Nanjing, China; Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, Research Unit of PK-PD Based Bioactive Components and Pharmacodynamic Target Discovery of Natural Medicine of Chinese Academy of Medical Sciences, China Pharmaceutical University, Nanjing, China.
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Laboratory of Drug Metabolism & Pharmacokinetics, China Pharmaceutical University, Nanjing, China.
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29
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Hibberd TJ, Ramsay S, Spencer-Merris P, Dinning PG, Zagorodnyuk VP, Spencer NJ. Circadian rhythms in colonic function. Front Physiol 2023; 14:1239278. [PMID: 37711458 PMCID: PMC10498548 DOI: 10.3389/fphys.2023.1239278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
A rhythmic expression of clock genes occurs within the cells of multiple organs and tissues throughout the body, termed "peripheral clocks." Peripheral clocks are subject to entrainment by a multitude of factors, many of which are directly or indirectly controlled by the light-entrainable clock located in the suprachiasmatic nucleus of the hypothalamus. Peripheral clocks occur in the gastrointestinal tract, notably the epithelia whose functions include regulation of absorption, permeability, and secretion of hormones; and in the myenteric plexus, which is the intrinsic neural network principally responsible for the coordination of muscular activity in the gut. This review focuses on the physiological circadian variation of major colonic functions and their entraining mechanisms, including colonic motility, absorption, hormone secretion, permeability, and pain signalling. Pathophysiological states such as irritable bowel syndrome and ulcerative colitis and their interactions with circadian rhythmicity are also described. Finally, the classic circadian hormone melatonin is discussed, which is expressed in the gut in greater quantities than the pineal gland, and whose exogenous use has been of therapeutic interest in treating colonic pathophysiological states, including those exacerbated by chronic circadian disruption.
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Affiliation(s)
- Timothy J. Hibberd
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Stewart Ramsay
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | | | - Phil G. Dinning
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
- Colorectal Surgical Unit, Division of Surgery, Flinders Medical Centre, Adelaide, SA, Australia
| | | | - Nick J. Spencer
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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30
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Wang B, Dunlap JC. Domains required for the interaction of the central negative element FRQ with its transcriptional activator WCC within the core circadian clock of Neurospora. J Biol Chem 2023; 299:104850. [PMID: 37220856 PMCID: PMC10320511 DOI: 10.1016/j.jbc.2023.104850] [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: 02/25/2023] [Revised: 05/04/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
In the negative feedback loop composing the Neurospora circadian clock, the core element, FREQUENCY (FRQ), binds with FRQ-interacting RNA helicase (FRH) and casein kinase 1 to form the FRQ-FRH complex (FFC) which represses its own expression by interacting with and promoting phosphorylation of its transcriptional activators White Collar-1 (WC-1) and WC-2 (together forming the White Collar complex, WCC). Physical interaction between FFC and WCC is a prerequisite for the repressive phosphorylations, and although the motif on WCC needed for this interaction is known, the reciprocal recognition motif(s) on FRQ remains poorly defined. To address this, we assessed FFC-WCC in a series of frq segmental-deletion mutants, confirming that multiple dispersed regions on FRQ are necessary for its interaction with WCC. Biochemical analysis shows that interaction between FFC and WCC but not within FFC or WCC can be disrupted by high salt, suggesting that electrostatic forces drive the association of the two complexes. As a basic sequence on WC-1 was previously identified as a key motif for WCC-FFC assembly, our mutagenetic analysis targeted negatively charged residues of FRQ, leading to identification of three Asp/Glu clusters in FRQ that are indispensable for FFC-WCC formation. Surprisingly, in several frq Asp/Glu-to-Ala mutants that vastly diminish FFC-WCC interaction, the core clock still oscillates robustly with an essentially wildtype period, indicating that the interaction between the positive and negative elements in the feedback loop is required for the operation of the circadian clock but is not a determinant of the period length.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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31
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Aye L, Wang Z, Chen F, Xiong Y, Zhou J, Wu F, Hu L, Wang D. Circadian Regulator-Mediated Molecular Subtypes Depict the Features of Tumor Microenvironment and Indicate Prognosis in Head and Neck Squamous Cell Carcinoma. J Immunol Res 2023; 2023:9946911. [PMID: 37342762 PMCID: PMC10279500 DOI: 10.1155/2023/9946911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/07/2022] [Indexed: 06/23/2023] Open
Abstract
Introduction Circadian rhythm is involved in multiple biological activities and implicated in cancer development. However, the role of circadian rhythm in head and neck squamous cell carcinoma (HNSCC) has not been fully interpreted yet. Herein, the present study set out to explore the significance of circadian regulator genes (CRGs) in HNSCC. Materials and Methods The molecular landscape and clinical significance of 13 CRGs in HNSCC were explored based on The Cancer Genome Atlas (TCGA). The biological functions of PER3, a key CRG, were validated by cellular experiments. The correlation of CRGs with microenvironment, pathway activities, and prognosis was determined by bioinformatic algorithms. A novel circadian score was introduced to evaluate the circadian modification pattern of each patient and further validated in an independent cohort from the Gene Expression Omnibus (GEO) dataset. Results CRGs presented high heterogeneity in HNSCC at both genomic and transcriptomic levels. Specifically, PER3 indicated a better prognosis and inhibited HNSCC cell proliferation. Moreover, HNSCC tissues displayed three circadian regulator patterns with distinct clinical outcomes, transcriptomic characteristics, and microenvironment features. Circadian score was an independent risk factor and exhibited excellent predictive efficiency in both the training cohort from the TCGA database and the validation cohort from the GEO database. Conclusions CRGs played an indispensable role in HNSCC development. An in-depth exploration of circadian rhythm would improve the understanding of HNSCC carcinogenesis and confer novel insights for future clinical practices.
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Affiliation(s)
- Ling Aye
- Department of Otolaryngology, Shanghai Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Zhanying Wang
- Five-Year Program Clinical Medicine, Grade of 2019, West China School of Medicine, Sichuan University, Chengdu, 610041 Sichuan, China
| | - Fanghua Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Yujun Xiong
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiaying Zhou
- Department of Otolaryngology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Feizhen Wu
- Laboratory of Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- Key Laboratory of Birth Defects, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Li Hu
- Department of Otolaryngology, Shanghai Eye & ENT Hospital, Fudan University, Shanghai 200031, China
| | - Dehui Wang
- Department of Otolaryngology, Shanghai Eye & ENT Hospital, Fudan University, Shanghai 200031, China
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32
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Philpott JM, Freeberg AM, Park J, Lee K, Ricci CG, Hunt SR, Narasimamurthy R, Segal DH, Robles R, Cai Y, Tripathi S, McCammon JA, Virshup DM, Chiu JC, Lee C, Partch CL. PERIOD phosphorylation leads to feedback inhibition of CK1 activity to control circadian period. Mol Cell 2023; 83:1677-1692.e8. [PMID: 37207626 DOI: 10.1016/j.molcel.2023.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 02/16/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023]
Abstract
PERIOD (PER) and Casein Kinase 1δ regulate circadian rhythms through a phosphoswitch that controls PER stability and repressive activity in the molecular clock. CK1δ phosphorylation of the familial advanced sleep phase (FASP) serine cluster embedded within the Casein Kinase 1 binding domain (CK1BD) of mammalian PER1/2 inhibits its activity on phosphodegrons to stabilize PER and extend circadian period. Here, we show that the phosphorylated FASP region (pFASP) of PER2 directly interacts with and inhibits CK1δ. Co-crystal structures in conjunction with molecular dynamics simulations reveal how pFASP phosphoserines dock into conserved anion binding sites near the active site of CK1δ. Limiting phosphorylation of the FASP serine cluster reduces product inhibition, decreasing PER2 stability and shortening circadian period in human cells. We found that Drosophila PER also regulates CK1δ via feedback inhibition through the phosphorylated PER-Short domain, revealing a conserved mechanism by which PER phosphorylation near the CK1BD regulates CK1 kinase activity.
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Affiliation(s)
- Jonathan M Philpott
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alfred M Freeberg
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jiyoung Park
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Kwangjun Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Clarisse G Ricci
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sabrina R Hunt
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rajesh Narasimamurthy
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
| | - David H Segal
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rafael Robles
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Yao Cai
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Sarvind Tripathi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - J Andrew McCammon
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | - Choogon Lee
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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Chen X, Liu X, Gan X, Li S, Ma H, Zhang L, Wang P, Li Y, Huang T, Yang X, Fang L, Liang Y, Wu J, Chen T, Zhou Z, Liu X, Guo J. Differential regulation of phosphorylation, structure and stability of circadian clock protein FRQ isoforms. J Biol Chem 2023; 299:104597. [PMID: 36898580 PMCID: PMC10140173 DOI: 10.1016/j.jbc.2023.104597] [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: 08/08/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 03/12/2023] Open
Abstract
Neurospora crassa is an important model for circadian clock research. The Neurospora core circadian component FRQ protein has two isoforms, large FRQ (l-FRQ) and small FRQ (s-FRQ), of which l-FRQ bears an additional N-terminal 99-amino acid fragment. However, how the FRQ isoforms operate differentially in regulating the circadian clock remains elusive. Here, we show l-FRQ and s-FRQ play different roles in regulating the circadian negative feedback loop. Compared to s-FRQ, l-FRQ is less stable at three temperatures, and undergoes hypophosphorylation and faster degradation. The phosphorylation of the C-terminal l-FRQ 794-aa fragment was markedly higher than that of s-FRQ, suggesting the l-FRQ N-terminal 99-aa region may regulate phosphorylation of the entire FRQ protein. Quantitative label-free LC/MS analysis identified several peptides that were differentially phosphorylated between l-FRQ and s-FRQ, which were distributed in FRQ in an interlaced fashion. Furthermore, we identified two novel phosphorylation sites, S765 and T781; mutations S765A and T781A showed no significant effects on conidiation rhythmicity, although T781 conferred FRQ stability. These findings demonstrate that FRQ isoforms play differential roles in the circadian negative feedback loop and undergo different regulation of phosphorylation, structure, and stability. The l-FRQ N-terminal 99-aa region plays an important role in regulating the phosphorylation, stability, conformation, and function of the FRQ protein. As the FRQ circadian clock counterparts in other species also have isoforms or paralogues, these findings will also further our understanding of the underlying regulatory mechanisms of the circadian clock in other organisms based on the high conservation of circadian clocks in eukaryotes.
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Affiliation(s)
- Xianyun Chen
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaolan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xihui Gan
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Silin Li
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huan Ma
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lin Zhang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Peiliang Wang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yunzhen Li
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tianyu Huang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaolin Yang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ling Fang
- Sun Yat-sen University Instrumental Analysis & Research Center, Sun Yat-sen University, Guangzhou 510006, China
| | - Yingying Liang
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingjing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tongyue Chen
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zengxuan Zhou
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiao Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinhu Guo
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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Wang B, Dunlap JC. Domains Required for FRQ-WCC Interaction within the Core Circadian Clock of Neurospora. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.25.530043. [PMID: 36865291 PMCID: PMC9980274 DOI: 10.1101/2023.02.25.530043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In the negative feedback loop composing the Neurospora circadian clock, the core element, FREQUENCY (FRQ) binds with FRH (FRQ-interacting RNA helicase) and Casein Kinase 1 (CK1) to form the FRQ-FRH complex (FFC) which represses its own expression by interacting with and promoting phosphorylation of its transcriptional activators White Collar-1 (WC-1) and WC-2 (together forming the White Collar Complex, WCC). Physical interaction between FFC and WCC is a prerequisite for the repressive phosphorylations, and although the motif on WCC needed for this interaction is known, the reciprocal recognition motif(s) on FRQ remains poorly defined. To address this, FFC-WCC was assessed in a series of frq segmental-deletion mutants, confirming that multiple dispersed regions on FRQ are necessary for its interaction with WCC. Biochemical analysis shows that interaction between FFC and WCC but not within FFC or WCC can be disrupted by high salt, suggesting that electrostatic forces drive the association of the two complexes. As a basic sequence on WC-1 was previously identified as a key motif for WCC-FFC assembly, our mutagenetic analysis targeted negatively charged residues of FRQ leading to identification of three Asp/Glu clusters in FRQ that are indispensable for FFC-WCC formation. Surprisingly, in several frq Asp/Glu-to-Ala mutants that vastly diminish FFC-WCC interaction, the core clock still oscillates robustly with an essentially WT period, indicating that the binding strength between the positive and negative elements in the feedback loop is required for the clock but is not a determinant of the period length.
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Wang B, Stevenson EL, Dunlap JC. Functional analysis of 110 phosphorylation sites on the circadian clock protein FRQ identifies clusters determining period length and temperature compensation. G3 (BETHESDA, MD.) 2023; 13:jkac334. [PMID: 36537198 PMCID: PMC9911066 DOI: 10.1093/g3journal/jkac334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/13/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
In the negative feedback loop driving the Neurospora circadian oscillator, the negative element, FREQUENCY (FRQ), inhibits its own expression by promoting phosphorylation of its heterodimeric transcriptional activators, White Collar-1 (WC-1) and WC-2. FRQ itself also undergoes extensive time-of-day-specific phosphorylation with over 100 phosphosites previously documented. Although disrupting individual or certain clusters of phosphorylation sites has been shown to alter circadian period lengths to some extent, it is still elusive how all the phosphorylations on FRQ control its activity. In this study, we systematically investigated the role in period determination of all 110 reported FRQ phosphorylation sites, using mutagenesis and luciferase reporter assays. Surprisingly, robust FRQ phosphorylation is still detected even when 84 phosphosites were eliminated altogether; further mutating another 26 phosphoresidues completely abolished FRQ phosphorylation. To identify phosphoresidue(s) on FRQ impacting circadian period length, a series of clustered frq phosphomutants covering all the 110 phosphosites were generated and examined for period changes. When phosphosites in the N-terminal and middle regions of FRQ were eliminated, longer periods were typically seen while removal of phosphorylation in the C-terminal tail resulted in extremely short periods, among the shortest reported. Interestingly, abolishing the 11 phosphosites in the C-terminal tail of FRQ not only results in an extremely short period, but also impacts temperature compensation (TC), yielding an overcompensated circadian oscillator. In addition, the few phosphosites in the middle of FRQ are also found to be crucial for TC. When different groups of FRQ phosphomutations were combined intramolecularly, expected additive effects were generally observed except for one novel case of intramolecular epistasis, where arrhythmicity resulting from one cluster of phosphorylation site mutants was restored by eliminating phosphorylation at another group of sites.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Elizabeth-Lauren Stevenson
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth College, Hanover, NH 03755, USA
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Cao X, Wang L, Selby CP, Lindsey-Boltz LA, Sancar A. Analysis of mammalian circadian clock protein complexes over a circadian cycle. J Biol Chem 2023; 299:102929. [PMID: 36682495 PMCID: PMC9950529 DOI: 10.1016/j.jbc.2023.102929] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
Circadian rhythmicity is maintained by a set of core clock proteins including the transcriptional activators CLOCK and BMAL1, and the repressors PER (PER1, PER2, and PER3), CRY (CRY1 and CRY2), and CK1δ. In mice, peak expression of the repressors in the early morning reduces CLOCK- and BMAL1-mediated transcription/translation of the repressors themselves. By late afternoon the repressors are largely depleted by degradation, and thereby their expression is reactivated in a cycle repeated every 24 h. Studies have characterized a variety of possible protein interactions and complexes associated with the function of this transcription-translation feedback loop. Our prior investigation suggested there were two circadian complexes responsible for rhythmicity, one containing CLOCK-BMAL and the other containing PER2, CRY1, and CK1δ. In this investigation, we acquired data from glycerol gradient centrifugation and gel filtration chromatography of mouse liver extracts obtained at different circadian times to further characterize circadian complexes. In addition, anti-PER2 and anti-CRY1 immunoprecipitates obtained from the same extracts were analyzed by liquid chromatography-tandem mass spectrometry to identify components of circadian complexes. Our results confirm the presence of discrete CLOCK-BMAL1 and PER-CRY-CK1δ complexes at the different circadian time points, provide masses of 255 and 707 kDa, respectively, for these complexes, and indicate that these complexes are composed principally of the core circadian proteins.
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Affiliation(s)
- Xuemei Cao
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Christopher P Selby
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Laura A Lindsey-Boltz
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA.
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Stanton D, Justin HS, Reitzel AM. Step in Time: Conservation of Circadian Clock Genes in Animal Evolution. Integr Comp Biol 2022; 62:1503-1518. [PMID: 36073444 DOI: 10.1093/icb/icac140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 01/05/2023] Open
Abstract
Over the past few decades, the molecular mechanisms responsible for circadian phenotypes of animals have been studied in increasing detail in mammals, some insects, and other invertebrates. Particular circadian proteins and their interactions are shared across evolutionary distant animals, resulting in a hypothesis for the canonical circadian clock of animals. As the number of species for which the circadian clockwork has been described increases, the circadian clock in animals driving cyclical phenotypes becomes less similar. Our focus in this review is to develop and synthesize the current literature to better understand the antiquity and evolution of the animal circadian clockwork. Here, we provide an updated understanding of circadian clock evolution in animals, largely through the lens of conserved genes characterized in the circadian clock identified in bilaterian species. These comparisons reveal extensive variation within the likely composition of the core clock mechanism, including losses of many genes, and that the ancestral clock of animals does not equate to the bilaterian clock. Despite the loss of these core genes, these species retain circadian behaviors and physiology, suggesting novel clocks have evolved repeatedly. Additionally, we highlight highly conserved cellular processes (e.g., cell division, nutrition) that intersect with the circadian clock of some animals. The conservation of these processes throughout the animal tree remains essentially unknown, but understanding their role in the evolution and maintenance of the circadian clock will provide important areas for future study.
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Affiliation(s)
- Daniel Stanton
- Department of Animal Sciences, University of Florida, Gainesville, FL 32608, USA
| | - Hannah S Justin
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte NC 28223, USA
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Blvd., Charlotte NC 28223, USA
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Gene-environment interaction between circadian clock gene polymorphisms and job stress on the risk of sleep disturbances. Psychopharmacology (Berl) 2022; 239:3337-3344. [PMID: 36031646 DOI: 10.1007/s00213-022-06219-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/21/2022] [Indexed: 10/15/2022]
Abstract
RATIONALE Sleep disturbances was associated with numerous adverse health outcomes. Many studies have reported that long-term exposure to job stress can lead to sleep disturbances, which may be influenced by genetic and environmental factors. OBJECTIVES This cross-sectional study investigated whether circadian clock gene polymorphisms modulated the influence of job stress on sleep disturbances in a Chinese Han population, which to our best knowledge has not been explored. METHODS The Effort-Reward Imbalance (ERI) scale and the Pittsburgh Sleep Quality Index (PSQI) were both used to access job stress and sleep disturbances. The SNaPshot SNP assay was carried out by screening for circadian clock gene polymorphisms in every participant. Interactions associated with sleep disturbances were assessed by linear hierarchical regression analysis and SPSS macros (PROCESS). RESULTS Linear hierarchical regression analysis showed that job stress was significantly related to sleep disturbances. Likewise, our study found a significant effect of PER2 rs2304672 polymorphisms on sleep disturbances (p < 0.01), after controlling for confounding factors. In addition, the PER2 rs2304672 genotype modulated the relationship between job stress and sleep disturbances (β = 0.414, p = 0.007). Interestingly, further analysis of the results of the PER2 gene rs2304672 × job stress interaction showed that rs2304672 G-allele carriers had a high-risk effect on sleep disturbances under high job stress. CONCLUSIONS Our results suggest that the PER2 rs2304672 polymorphism may modulate the influence of job stress on sleep disturbances. These findings contribute to the field of sleep disturbances prevention and treatment.
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Liang M, Dong L, Deng YZ. Circadian Redox Rhythm in Plant-Fungal Pathogen Interactions. Antioxid Redox Signal 2022; 37:726-738. [PMID: 35044223 DOI: 10.1089/ars.2021.0281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Significance: Circadian-controlled cellular growth, differentiation, and metabolism are mainly achieved by a classical transcriptional-translational feedback loop (TTFL), as revealed by investigations in animals, plants, and fungi. Recent Advances: Recently, reactive oxygen species (ROS) have been reported as part of a cellular network synchronizing nontranscriptional oscillators with established TTFL components, adding complexity to regulatory mechanisms of circadian rhythm. Both circadian rhythm and ROS homeostasis have a great impact on plant immunity as well as fungal pathogenicity, therefore interconnections of these two factors are implicit in plant-fungus interactions. Critical Issues: In this review, we aim to summarize the recent advances in circadian-controlled ROS homeostasis, or ROS-modulated circadian clock, in plant-fungus pathosystems, particularly using the rice (Oryza sativa) blast fungus (Magnaporthe oryzae) pathosystem as an example. Understanding of such bidirectional interaction between the circadian timekeeping machinery and ROS homeostasis/signaling would provide a theoretical basis for developing disease control strategies for important plants/crops. Future Directions: Questions remain unanswered about the detailed mechanisms underlying circadian regulation of redox homeostasis in M. oryzae, and the consequent fungal differentiation and death in a time-of-day manner. We believe that the rice-M. oryzae pathobiosystem would provide an excellent platform for investigating such issues in circadian-ROS interconnections in a plant-fungus interaction context. Antioxid. Redox Signal. 37, 726-738.
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Affiliation(s)
- Meiling Liang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Lihong Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Yi Zhen Deng
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
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40
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Abdalla OHMH, Mascarenhas B, Cheng HYM. Death of a Protein: The Role of E3 Ubiquitin Ligases in Circadian Rhythms of Mice and Flies. Int J Mol Sci 2022; 23:ijms231810569. [PMID: 36142478 PMCID: PMC9502492 DOI: 10.3390/ijms231810569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/04/2022] Open
Abstract
Circadian clocks evolved to enable organisms to anticipate and prepare for periodic environmental changes driven by the day–night cycle. This internal timekeeping mechanism is built on autoregulatory transcription–translation feedback loops that control the rhythmic expression of core clock genes and their protein products. The levels of clock proteins rise and ebb throughout a 24-h period through their rhythmic synthesis and destruction. In the ubiquitin–proteasome system, the process of polyubiquitination, or the covalent attachment of a ubiquitin chain, marks a protein for degradation by the 26S proteasome. The process is regulated by E3 ubiquitin ligases, which recognize specific substrates for ubiquitination. In this review, we summarize the roles that known E3 ubiquitin ligases play in the circadian clocks of two popular model organisms: mice and fruit flies. We also discuss emerging evidence that implicates the N-degron pathway, an alternative proteolytic system, in the regulation of circadian rhythms. We conclude the review with our perspectives on the potential for the proteolytic and non-proteolytic functions of E3 ubiquitin ligases within the circadian clock system.
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Affiliation(s)
- Osama Hasan Mustafa Hasan Abdalla
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Brittany Mascarenhas
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
- Correspondence:
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Noh SG, Jung HJ, Kim S, Arulkumar R, Kim DH, Park D, Chung HY. Regulation of Circadian Genes Nr1d1 and Nr1d2 in Sex-Different Manners during Liver Aging. Int J Mol Sci 2022; 23:ijms231710032. [PMID: 36077427 PMCID: PMC9456386 DOI: 10.3390/ijms231710032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Circadian rhythm is associated with the aging process and sex differences; however, how age and sex can change circadian regulation systems remains unclear. Thus, we aimed to evaluate age- and sex-related changes in gene expression and identify sex-specific target molecules that can regulate aging. Methods: Rat livers were categorized into four groups, namely, young male, old male, young female, and old female, and the expression of several genes involved in the regulation of the circadian rhythm was confirmed by in silico and in vitro studies. Results: Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses showed that the expression of genes related to circadian rhythms changed more in males than in females during liver aging. In addition, differentially expressed gene analysis and quantitative real-time polymerase chain reaction/western blotting analysis revealed that Nr1d1 and Nr1d2 expression was upregulated in males during liver aging. Furthermore, the expression of other circadian genes, such as Arntl, Clock, Cry1/2, Per1/2, and Rora/c, decreased in males during liver aging; however, these genes showed various gene expression patterns in females during liver aging. Conclusions: Age-related elevation of Nr1d1/2 downregulates the expression of other circadian genes in males, but not females, during liver aging. Consequently, age-related upregulation of Nr1d1/2 may play a more crucial role in the change in circadian rhythms in males than in females during liver aging.
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Affiliation(s)
- Sang Gyun Noh
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
- Department of Pharmacy, College of Pharmacy, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
| | - Hee Jin Jung
- Department of Pharmacy, College of Pharmacy, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
| | - Seungwoo Kim
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
- Department of Pharmacy, College of Pharmacy, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
| | - Radha Arulkumar
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
- Department of Pharmacy, College of Pharmacy, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
| | - Dae Hyun Kim
- Department of Pharmacy, College of Pharmacy, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
| | - Daeui Park
- Department of Predictive Toxicology, Korea Institute of Toxicology, 141, Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea
| | - Hae Young Chung
- Interdisciplinary Research Program of Bioinformatics and Longevity Science, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
- Department of Pharmacy, College of Pharmacy, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2814
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42
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Rasmussen ES, Takahashi JS, Green CB. Time to target the circadian clock for drug discovery. Trends Biochem Sci 2022; 47:745-758. [PMID: 35577675 PMCID: PMC9378619 DOI: 10.1016/j.tibs.2022.04.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
The circadian clock is an intracellular timekeeping device that drives daily rhythms in diverse and extensive processes throughout the body. The clock mechanism comprises a core transcription/translation negative feedback loop that is modulated by a complex set of additional interlocking feedback loops. Pharmacological manipulation of the clock may be valuable for treating many maladies including jet lag, shift work and related sleep disorders, various metabolic diseases, and cancer. We review recent identification of small-molecule clock modulators and discuss the biochemical features of the core clock that may be amenable to future drug discovery.
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Affiliation(s)
- Emil Sjulstok Rasmussen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Bazhanova ED. Desynchronosis: Types, Main Mechanisms, Role in the Pathogenesis of Epilepsy and Other Diseases: A Literature Review. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081218. [PMID: 36013397 PMCID: PMC9410012 DOI: 10.3390/life12081218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/31/2022] [Accepted: 08/09/2022] [Indexed: 11/21/2022]
Abstract
Circadian information is stored in mammalian tissues by an autonomous network of transcriptional feedback loops that have evolved to optimally regulate tissue-specific functions. Currently, stable circadian rhythms of the expression of clock genes (Bmal1/Per2/Cry1, etc.), hormones, and metabolic genes (Glut4/leptin, etc.) have been demonstrated. Desynchronoses are disorders of the body’s biorhythms, where the direction and degree of shift of various indicators of the oscillatory process are disturbed. Desynchronosis can be caused by natural conditions or man-made causes. The disruption of circadian rhythms is a risk factor for the appearance of physiological and behavioral disorders and the development of diseases, including epilepsy, and metabolic and oncological diseases. Evidence suggests that seizure activity in the epilepsy phenotype is associated with circadian dysfunction. Interactions between epilepsy and circadian rhythms may be mediated through melatonin, sleep–wake cycles, and clock genes. The correction of circadian dysfunction can lead to a decrease in seizure activity and vice versa. Currently, attempts are being made to pharmacologically correct desynchronosis and related psycho-emotional disorders, as well as combined somatic pathology. On the other hand, the normalization of the light regimen, the regulation of sleep–wake times, and phototherapy as additions to standard treatment can speed up the recovery of patients with various diseases.
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Affiliation(s)
- Elena D. Bazhanova
- Laboratory of Comparative Biochemistry of Cell Function, Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia; ; Tel.: +7-9119008134
- Laboratory of Morphology and Electron Microscopy, Golikov Research Center of Toxicology, 192019 St. Petersburg, Russia
- Laboratory of Apoptosis Studying, Astrakhan State University, 414040 Astrakhan, Russia
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44
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The duper mutation reveals previously unsuspected functions of Cryptochrome 1 in circadian entrainment and heart disease. Proc Natl Acad Sci U S A 2022; 119:e2121883119. [PMID: 35930669 PMCID: PMC9371649 DOI: 10.1073/pnas.2121883119] [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] [Indexed: 02/07/2023] Open
Abstract
The Cryptochrome 1 (Cry1)-deficient duper mutant hamster has a short free-running period in constant darkness (τDD) and shows large phase shifts in response to brief light pulses. We tested whether this measure of the lability of the circadian phase is a general characteristic of Cry1-null animals and whether it indicates resistance to jet lag. Upon advance of the light:dark (LD) cycle, both duper hamsters and Cry1-/- mice re-entrained locomotor rhythms three times as fast as wild types. However, accelerated re-entrainment was dissociated from the amplified phase-response curve (PRC): unlike duper hamsters, Cry1-/- mice show no amplification of the phase response to 15' light pulses. Neither the amplified acute shifts nor the increased rate of re-entrainment in duper mutants is due to acceleration of the circadian clock: when mutants drank heavy water to lengthen the period, these aspects of the phenotype persisted. In light of the health consequences of circadian misalignment, we examined effects of duper and phase shifts on a hamster model of heart disease previously shown to be aggravated by repeated phase shifts. The mutation shortened the lifespan of cardiomyopathic hamsters relative to wild types, but this effect was eliminated when mutants experienced 8-h phase shifts every second week, to which they rapidly re-entrained. Our results reveal previously unsuspected roles of Cry1 in phase shifting and longevity in the face of heart disease. The duper mutant offers new opportunities to understand the basis of circadian disruption and jet lag.
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45
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Parlak GC, Camur BB, Gul S, Ozcan O, Baris I, Kavakli IH. The secondary pocket of Cryptochrome 2 is important for the regulation of its stability and localization. J Biol Chem 2022; 298:102334. [PMID: 35933018 PMCID: PMC9442382 DOI: 10.1016/j.jbc.2022.102334] [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: 03/22/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/28/2022] Open
Abstract
Human clock-gene variations contribute to the phenotypic differences observed in various behavioral and physiological processes such as diurnal preference, sleep, metabolism, mood regulation, addiction, and fertility. However, little is known about the possible effects of identified variations at the molecular level. In this study, we performed a functional characterization at the cellular level of rare CRYPTOCHROME 2 (CRY2) missense variations that were identified from the Ensembl database. Our structural studies revealed that three variations (p.Pro123Leu, p.Asp406His, p.Ser410Ile) are located at the rim of the secondary pocket of CRY2. We show these variants were unable to repress CLOCK/BMAL1-driven transcription in a cell-based reporter assay and had reduced affinity to CLOCK/BMAL1. Furthermore, our biochemical studies indicated that the variants were less stable than the wild-type CRY2, which could be rescued in the presence of Period 2 (PER2), another core clock protein. Finally, we found these variants were unable to properly localize to the nucleus, and thereby were unable to rescue the circadian rhythm in a Cry1-/-Cry2-/- double-knockout mouse embryonic fibroblast cell line. Collectively, our data suggest that the rim of the secondary pocket of CRY2 plays a significant role in its nuclear localization independently of PER2 and in the intact circadian rhythm at the cellular level.
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Affiliation(s)
- Gizem Cagla Parlak
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Bilge Bahar Camur
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Seref Gul
- Istanbul University, Department of Biology, Biotechnology Division, 34134 Suleymaniye, Istanbul, Turkey
| | - Onur Ozcan
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Ibrahim Baris
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Koc university Department Molecular Biology and Genetics, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey; Koc university Department Chemical and Biological Engineering, Rumeli Feneri Yolu, Sariyer, Istanbul, Turkey.
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46
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Sanford ABA, da Cunha LS, Machado CB, de Pinho Pessoa FMC, Silva ANDS, Ribeiro RM, Moreira FC, de Moraes Filho MO, de Moraes MEA, de Souza LEB, Khayat AS, Moreira-Nunes CA. Circadian Rhythm Dysregulation and Leukemia Development: The Role of Clock Genes as Promising Biomarkers. Int J Mol Sci 2022; 23:ijms23158212. [PMID: 35897788 PMCID: PMC9332415 DOI: 10.3390/ijms23158212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022] Open
Abstract
The circadian clock (CC) is a daily system that regulates the oscillations of physiological processes and can respond to the external environment in order to maintain internal homeostasis. For the functioning of the CC, the clock genes (CG) act in different metabolic pathways through the clock-controlled genes (CCG), providing cellular regulation. The CC’s interruption can result in the development of different diseases, such as neurodegenerative and metabolic disorders, as well as cancer. Leukemias correspond to a group of malignancies of the blood and bone marrow that occur when alterations in normal cellular regulatory processes cause the uncontrolled proliferation of hematopoietic stem cells. This review aimed to associate a deregulated CC with the manifestation of leukemia, looking for possible pathways involving CG and their possible role as leukemic biomarkers.
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Affiliation(s)
- Ana Beatriz Aguiar Sanford
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil; (A.B.A.S.); (L.S.d.C.)
| | - Leidivan Sousa da Cunha
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil; (A.B.A.S.); (L.S.d.C.)
| | - Caio Bezerra Machado
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Flávia Melo Cunha de Pinho Pessoa
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Abigail Nayara dos Santos Silva
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
| | | | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
| | - Manoel Odorico de Moraes Filho
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Maria Elisabete Amaral de Moraes
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
| | - Lucas Eduardo Botelho de Souza
- Center for Cell-Based Therapy, Regional Blood Center of Ribeirão Preto, University of São Paulo, São Paulo 14051-140, SP, Brazil;
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
| | - Caroline Aquino Moreira-Nunes
- Unichristus University Center, Faculty of Biomedicine, Fortaleza 60430-275, CE, Brazil; (A.B.A.S.); (L.S.d.C.)
- Pharmacogenetics Laboratory, Department of Medicine, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (C.B.M.); (F.M.C.d.P.P.); (M.O.d.M.F.); (M.E.A.d.M.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (A.N.d.S.S.); (F.C.M.); (A.S.K.)
- Northeast Biotechnology Network (RENORBIO), Itaperi Campus, Ceará State University, Fortaleza 60740-903, CE, Brazil
- Correspondence:
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47
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Narayanan V, Rodrigues AL, Dordick JS. Influence of Circadian Rhythm on Drug Metabolism in 3D Hepatic Spheroids. Biotechnol Bioeng 2022; 119:2842-2856. [PMID: 35822281 DOI: 10.1002/bit.28180] [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: 04/08/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022]
Abstract
Circadian rhythms are characterized as oscillations that fluctuate based on a 24h cycle and are responsible for regulation of physiological functions. While the internal clock synchronizes gene expression using external cues like light, a similar synchronization can be induced in vitro by incubating the cells with an increased percentage of serum followed by its rapid removal. Previous studies have suggested that synchronization of HepG2 cell line induced the rhythmic expression of drug metabolizing enzymes (DME) most specifically the cytochrome P450 enzymes. However, there is a lack of evidence demonstrating the influence of 3D microenvironment on the rhythmicity of these genes. To understand this interplay, gene expression of the circadian machinery and CYP450s were compared using the model human hepatocarcinoma cell line, HepG2. Upon serum shock synchronization, gene and protein expression of core clock regulators was assessed and rhythmic expression of these genes was demonstrated. Further insight into the interrelations between various gene pairs was obtained using statistical analysis. Using RNA sequencing, an in-depth understanding of the widespread effects of circadian regulation on genes involved in metabolic processes in the liver was obtained. This study aids in the better understanding of chronopharmacokinetic events in humans using physiologically relevant 3D culture systems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vibha Narayanan
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Andre L Rodrigues
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.,Departments of Biological Sciences and Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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48
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An Y, Yuan B, Xie P, Gu Y, Liu Z, Wang T, Li Z, Xu Y, Liu Y. Decoupling PER phosphorylation, stability and rhythmic expression from circadian clock function by abolishing PER-CK1 interaction. Nat Commun 2022; 13:3991. [PMID: 35810166 PMCID: PMC9271041 DOI: 10.1038/s41467-022-31715-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/29/2022] [Indexed: 11/09/2022] Open
Abstract
Robust rhythms of abundances and phosphorylation profiles of PERIOD proteins were thought be the master rhythms that drive mammalian circadian clock functions. PER stability was proposed to be a major determinant of period length. In mammals, CK1 forms stable complexes with PER. Here we identify the PER residues essential for PER-CK1 interaction. In cells and in mice, their mutation abolishes PER phosphorylation and CLOCK hyperphosphorylation, resulting in PER stabilization, arrhythmic PER abundance and impaired negative feedback process, indicating that PER acts as the CK1 scaffold in circadian feedback mechanism. Surprisingly, the mutant mice exhibit robust short period locomotor activity and other physiological rhythms but low amplitude molecular rhythms. PER-CK1 interaction has two opposing roles in regulating CLOCK-BMAL1 activity. These results indicate that the circadian clock can function independently of PER phosphorylation and abundance rhythms due to another PER-CRY-dependent feedback mechanism and that period length can be uncoupled from PER stability.
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Affiliation(s)
- Yang An
- Model Animal Research Center, Nanjing University, 12 Xuefu Road, Pukou District, Nanjing, 210061, China.,Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Baoshi Yuan
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Pancheng Xie
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China.,Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yue Gu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhiwei Liu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Tao Wang
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Zhihao Li
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China
| | - Ying Xu
- Cambridge-Su Genomic Resource Center, Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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49
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Wang AS, Steers NJ, Parab AR, Gachon F, Sweet MJ, Mysorekar IU. Timing is everything: impact of development, ageing and circadian rhythm on macrophage functions in urinary tract infections. Mucosal Immunol 2022; 15:1114-1126. [PMID: 36038769 DOI: 10.1038/s41385-022-00558-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 02/04/2023]
Abstract
The bladder supports a diversity of macrophage populations with functional roles related to homeostasis and host defense, including clearance of cell debris from tissue, immune surveillance, and inflammatory responses. This review examines these roles with particular attention given to macrophage origins, differentiation, recruitment, and engagement in host defense against urinary tract infections (UTIs), where these cells recognize uropathogens through a combination of receptor-mediated responses. Time is an important variable that is often overlooked in many clinical and biological studies, including in relation to macrophages and UTIs. Given that ageing is a significant factor in urinary tract infection pathogenesis and macrophages have been shown to harbor their own circadian system, this review also explores the influence of age on macrophage functions and the role of diurnal variations in macrophage functions in host defense and inflammation during UTIs. We provide a conceptual framework for future studies that address these key knowledge gaps.
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Affiliation(s)
- Alison S Wang
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, QLD, Australia.,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
| | - Nicholas J Steers
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
| | - Adwaita R Parab
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Frédéric Gachon
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, QLD, Australia
| | - Matthew J Sweet
- Institute for Molecular Bioscience (IMB) and IMB Centre for Inflammation and Disease Research, The University of Queensland, St. Lucia, QLD, Australia. .,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia.
| | - Indira U Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA. .,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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50
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Clavere NG, Alqallaf A, Rostron KA, Parnell A, Mitchell R, Patel K, Boateng SY. Inhibition of activin A receptor signalling attenuates age-related pathological cardiac remodelling. Dis Model Mech 2022; 15:275323. [PMID: 35380160 PMCID: PMC9118092 DOI: 10.1242/dmm.049424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/16/2022] [Indexed: 11/20/2022] Open
Abstract
In the heart, ageing is associated with DNA damage, oxidative stress, fibrosis and activation of the activin signalling pathway, leading to cardiac dysfunction. The cardiac effects of activin signalling blockade in progeria are unknown. This study investigated the cardiac effects of progeria induced by attenuated levels of Ercc1, which is required for DNA excision and repair, and the impact of activin signalling blockade using a soluble activin receptor type IIB (sActRIIB). DNA damage and oxidative stress were significantly increased in Ercc1Δ/− hearts, but were reduced by sActRIIB treatment. sActRIIB treatment improved cardiac systolic function and induced cardiomyocyte hypertrophy in Ercc1Δ/− hearts. RNA-sequencing analysis showed that in Ercc1Δ/− hearts, there was an increase in pro-oxidant and a decrease in antioxidant gene expression, whereas sActRIIB treatment reversed this effect. Ercc1Δ/− hearts also expressed higher levels of anti-hypertrophic genes and decreased levels of pro-hypertrophic ones, which were also reversed by sActRIIB treatment. These results show for the first time that inhibition of activin A receptor signalling attenuates cardiac dysfunction, pathological tissue remodelling and gene expression in Ercc1-deficient mice and presents a potentially novel therapeutic target for heart diseases. Summary: Attenuated DNA repair is associated with pathological cardiac remodelling and gene expression. Much of this phenotype is attenuated by inhibition of the activin signalling pathway using soluble activin receptor treatment.
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Affiliation(s)
- Nicolas G Clavere
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Ali Alqallaf
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Kerry A Rostron
- Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Commonwealth Building, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Andrew Parnell
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Robert Mitchell
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Ketan Patel
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
| | - Samuel Y Boateng
- Institute of Cardiovascular and Metabolic Research, School of Biological Sciences, Health and Life Sciences Building, University of Reading, Whiteknights, Reading RG6 6UB, UK
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