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Bartölke R, Nießner C, Reinhard K, Wolfrum U, Meimann S, Bolte P, Feederle R, Mouritsen H, Dedek K, Peichl L, Winklhofer M. Full-Length Cryptochrome 1 in the Outer Segments of the Retinal Blue Cone Photoreceptors in Humans and Great Apes Suggests a Role Beyond Transcriptional Repression. FASEB J 2025; 39:e70523. [PMID: 40277221 PMCID: PMC12023722 DOI: 10.1096/fj.202402614r] [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: 11/05/2024] [Revised: 02/07/2025] [Accepted: 03/27/2025] [Indexed: 04/26/2025]
Abstract
Mammalian cryptochrome 1 (CRY1) is a central player in the circadian transcription-translation feedback loop, crucial for maintaining a roughly 24-h rhythm. CRY1 was suggested to also function as a blue-light photoreceptor in humans and has been found to be expressed at the mRNA level in various cell types of the inner retina. However, attempts to detect CRY1 at the protein level in the human retina have remained unsuccessful so far. Using various C-terminal specific antibodies recognizing full-length CRY1 protein, we consistently detected selective labeling in the outer segments of short wavelength-sensitive (SWS1, "blue") cone photoreceptor cells across human, bonobo, and gorilla retinae. No other retinal cell types were stained, which is in contrast to what would be expected of a ubiquitous clock protein. Subcellular fractionation experiments in transfected HEK cells using a C-terminal specific antibody located full-length CRY1 in the cytosol and membrane fractions. Our findings indicate that human CRY1 has several different functions including at least one nonclock function. Our results also raise the likely possibility that several different versions of CRY1 exist in humans. We suggest that truncation of the C-terminal tail, maybe to different degrees, may affect the localization and function of human CRY1.
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Affiliation(s)
- Rabea Bartölke
- Institute for Biology and Environmental Sciences (IBU)Carl von Ossietzky University of OldenburgOldenburgGermany
| | - Christine Nießner
- Max Planck Institute for Brain ResearchFrankfurt am MainGermany
- Ernst Strüngmann Institute for NeuroscienceFrankfurt am MainGermany
| | - Katja Reinhard
- Retinal Circuits and Optogenetics, Centre for Integrative Neuroscience and Bernstein Center for Computational NeuroscienceUniversity of TübingenTübingenGermany
- Neuroscience Graduate SchoolUniversity of TübingenTübingenGermany
- Scuola Internazionale Superiore di Studi Avanzati (SISSA)TriesteItaly
| | - Uwe Wolfrum
- Institute of Molecular PhysiologyJohannes Gutenberg UniversityMainzGermany
| | - Sonja Meimann
- Institute of Cellular and Molecular AnatomyDr. Senckenberg Anatomy, Goethe UniversityFrankfurt am MainGermany
| | - Petra Bolte
- Institute for Biology and Environmental Sciences (IBU)Carl von Ossietzky University of OldenburgOldenburgGermany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH)NeuherbergGermany
| | - Henrik Mouritsen
- Institute for Biology and Environmental Sciences (IBU)Carl von Ossietzky University of OldenburgOldenburgGermany
- Forschungszentrum Neurosensorik, Carl von Ossietzky Universität OldenburgOldenburgGermany
| | - Karin Dedek
- Institute for Biology and Environmental Sciences (IBU)Carl von Ossietzky University of OldenburgOldenburgGermany
- Forschungszentrum Neurosensorik, Carl von Ossietzky Universität OldenburgOldenburgGermany
| | - Leo Peichl
- Max Planck Institute for Brain ResearchFrankfurt am MainGermany
- Ernst Strüngmann Institute for NeuroscienceFrankfurt am MainGermany
- Institute of Cellular and Molecular AnatomyDr. Senckenberg Anatomy, Goethe UniversityFrankfurt am MainGermany
- Institute of Clinical NeuroanatomyDr. Senckenberg Anatomy, Goethe UniversityFrankfurt am MainGermany
| | - Michael Winklhofer
- Institute for Biology and Environmental Sciences (IBU)Carl von Ossietzky University of OldenburgOldenburgGermany
- Forschungszentrum Neurosensorik, Carl von Ossietzky Universität OldenburgOldenburgGermany
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2
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Majewska M, Hanić M, Bartölke R, Schmidt J, Bożek J, Gerhards L, Mouritsen H, Koch KW, Solov’yov IA, Brand I. European Robin Cryptochrome-4a Associates with Lipid Bilayers in an Ordered Manner, Fulfilling a Molecular-Level Condition for Magnetoreception. ACS Chem Biol 2025; 20:592-606. [PMID: 39982451 PMCID: PMC11934094 DOI: 10.1021/acschembio.4c00576] [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: 08/31/2024] [Revised: 01/26/2025] [Accepted: 01/30/2025] [Indexed: 02/22/2025]
Abstract
Since the middle of the 20th century, long-distance avian migration has been known to rely partly on geomagnetic field. However, the underlying sensory mechanism is still not fully understood. Cryptochrome-4a (ErCry4a), found in European robin (Erithacus rubecula), a night-migratory songbird, has been suggested to be a magnetic sensory molecule. It is sensitive to external magnetic fields via the so-called radical-pair mechanism. ErCry4a is primarily located in the outer segments of the double-cone photoreceptor cells in the eye, which contain stacked and highly ordered membranes that could facilitate the anisotropic attachment of ErCry4a needed for magnetic compass sensing. Here, we investigate possible interactions of ErCry4a with a model membrane that mimics the lipid composition of outer segments of vertebrate photoreceptor cells using experimental and computational approaches. Experimental results show that the attachment of ErCry4a to the membrane could be controlled by the physical state of lipid molecules (average area per lipid) in the outer leaflet of the lipid bilayer. Furthermore, polarization modulation infrared reflection absorption spectroscopy allowed us to determine the conformation, motional freedom, and average orientation of the α-helices in ErCry4a in a membrane-associated state. Atomistic molecular dynamics studies supported the experimental results. A ∼ 1000 kcal mol-1 decrease in the interaction energy as a result of ErCry4a membrane binding was determined compared to cases where no protein binding to the membrane occurred. At the molecular level, the binding seems to involve negatively charged carboxylate groups of the phosphoserine lipids and the C-terminal residues of ErCry4a. Our study reveals a potential direct interaction of ErCry4a with the lipid membrane and discusses how this binding could be an essential step for ErCry4a to propagate a magnetic signal further and thus fulfill a role as a magnetoreceptor.
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Affiliation(s)
- Marta Majewska
- Institute
of Chemistry, School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - Maja Hanić
- Institute
of Physics, School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - Rabea Bartölke
- Animal
Navigation, Institute of Biology and Environmental Sciences, School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Oldenburg D-26111, Germany
| | - Jessica Schmidt
- Animal
Navigation, Institute of Biology and Environmental Sciences, School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Oldenburg D-26111, Germany
| | - Justyna Bożek
- Institute
of Chemistry, School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - Luca Gerhards
- Institute
of Physics, School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - Henrik Mouritsen
- Animal
Navigation, Institute of Biology and Environmental Sciences, School
of Mathematics and Science, Carl von Ossietzky
Universität Oldenburg, Oldenburg D-26111, Germany
- Research
Center for Neurosensory Sciences, Carl von
Ossietzky Universität Oldenburg, Oldenburg D-26111, Germany
| | - Karl-Wilhelm Koch
- Research
Center for Neurosensory Sciences, Carl von
Ossietzky Universität Oldenburg, Oldenburg D-26111, Germany
- Division
of Biochemistry, Department of Neuroscience, Carl von Ossietzky Universität Oldenburg, Oldenburg D-26111, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
- Research
Center for Neurosensory Sciences, Carl von
Ossietzky Universität Oldenburg, Oldenburg D-26111, Germany
- Institute
of Physics, Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Oldenburg 26129, Germany
| | - Izabella Brand
- Institute
of Chemistry, School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
- Research
Center for Neurosensory Sciences, Carl von
Ossietzky Universität Oldenburg, Oldenburg D-26111, Germany
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3
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Yin D, Zhong Z, Zeng F, Xu Z, Li J, Ren W, Yang G, Wang H, Xu S. Evolution of canonical circadian clock genes underlies unique sleep strategies of marine mammals for secondary aquatic adaptation. PLoS Genet 2025; 21:e1011598. [PMID: 40101169 PMCID: PMC11919277 DOI: 10.1371/journal.pgen.1011598] [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: 07/31/2024] [Accepted: 01/28/2025] [Indexed: 03/20/2025] Open
Abstract
To satisfy the needs of sleeping underwater, marine mammals, including cetaceans, sirenians, and pinnipeds, have evolved an unusual form of sleep, known as unihemispheric slow-wave sleep (USWS), in which one brain hemisphere is asleep while the other is awake. All aquatic cetaceans have only evolved USWS without rapid eye movement (REM) sleep, whereas aquatic sirenians and amphibious pinnipeds display both bihemispheric slow-wave sleep (BSWS) and USWS, as well as REM sleep. However, the molecular genetic changes underlying USWS remain unknown. The present study investigated the evolution of eight canonical circadian genes and found that positive selection occurred mainly within cetacean lineages. Furthermore, convergent evolution was observed in lineages with USWS at three circadian clock genes. Remarkably, in vitro assays showed that cetacean-specific mutations increased the nuclear localization of zebrafish clocka, and enhanced the transcriptional activation activity of Clocka and Bmal1a. In vivo, transcriptome analysis showed that the overexpression of the cetacean-specific mutant clocka (clocka-mut) caused the upregulation of the wakefulness-promoting glutamatergic genes and the differential expression of multiple genes associated with sleep regulation. In contrast, the GABAergic and cholinergic pathways, which play important roles in promoting sleep, were downregulated in the bmal1a-mut-overexpressing zebrafish. Concordantly, sleep time of zebrafish overexpressing clocka-mut and bmal1a-mut were significantly less than the zebrafish overexpressing the wild-type genes, respectively. These findings support our hypothesis that canonical circadian clock genes may have evolved adaptively to enhance circadian regulation ability relating to sleep in cetaceans and, in turn, contribute to the formation of USWS.
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Affiliation(s)
- Daiqing Yin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Zhaomin Zhong
- Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, PR China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, PR China
| | - Fan Zeng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhikang Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, China
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou, Jiangsu, PR China
- School of Biology & Basic Medical Sciences, Suzhou Medical College, Soochow University, Suzhou, Jiangsu, PR China
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Zeng D, Lv J, Li X, Liu H. The Arabidopsis blue-light photoreceptor CRY2 is active in darkness to inhibit root growth. Cell 2025; 188:60-76.e20. [PMID: 39549699 DOI: 10.1016/j.cell.2024.10.031] [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: 07/19/2024] [Revised: 09/16/2024] [Accepted: 10/16/2024] [Indexed: 11/18/2024]
Abstract
Cryptochromes (CRYs) are blue-light receptors that regulate diverse aspects of plant growth. However, whether and how non-photoexcited CRYs function in darkness or non-blue-light conditions is unknown. Here, we show that CRY2 affects the Arabidopsis transcriptome even in darkness, revealing a non-canonical function. CRY2 suppresses cell division in the root apical meristem to downregulate root elongation in darkness. Blue-light oligomerizes CRY2 to de-repress root elongation. CRY2 physically interacts with FORKED-LIKE 1 (FL1) and FL3, and these interactions are inhibited by blue light, with only monomeric but not dimeric CRY2 able to interact. FL1 and FL3 associate with the chromatin of cell division genes to facilitate their transcription. This pro-growth activity is inhibited by CRY2's physical interaction with FLs in darkness. Plants have evolved to perceive both blue-light and dark cues to coordinate activation and repression of competing developmental processes in above- and below-ground organs through economical and dichotomous use of ancient light receptors.
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Affiliation(s)
- Desheng Zeng
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China; University of Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Junqing Lv
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China; University of Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Xu Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China
| | - Hongtao Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, People's Republic of China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.
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Wang Z, Wang S, Bi Y, Boiti A, Zhang S, Vallone D, Lan X, Foulkes NS, Zhao H. Light-regulated microRNAs shape dynamic gene expression in the zebrafish circadian clock. PLoS Genet 2025; 21:e1011545. [PMID: 39777894 PMCID: PMC11750094 DOI: 10.1371/journal.pgen.1011545] [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: 06/20/2024] [Revised: 01/21/2025] [Accepted: 12/17/2024] [Indexed: 01/11/2025] Open
Abstract
A key property of the circadian clock is that it is reset by light to remain synchronized with the day-night cycle. An attractive model to explore light input to the circadian clock in vertebrates is the zebrafish. Circadian clocks in zebrafish peripheral tissues and even zebrafish-derived cell lines are entrainable by direct light exposure thus providing unique insight into the function and evolution of light regulatory pathways. Our previous work has revealed that light-induced gene transcription is a key step in the entrainment of the circadian clock as well as enabling the more general adaptation of zebrafish cells to sunlight exposure. However, considerable evidence points to post-transcriptional regulatory mechanisms, notably microRNAs (miRNAs), playing an essential role in shaping dynamic changes in mRNA levels. Therefore, does light directly impact the function of miRNAs? Are there light-regulated miRNAs and if so, which classes of mRNA do they target? To address these questions, we performed a complete sequencing analysis of light-induced changes in the zebrafish transcriptome, encompassing small non-coding RNAs as well as mRNAs. Importantly, we identified sets of light-regulated miRNAs, with many regulatory targets representing light-inducible mRNAs including circadian clock genes and genes involved in redox homeostasis. We subsequently focused on the light-responsive miR-204-3-3p and miR-430a-3p which are predicted to regulate the expression of cryptochrome genes (cry1a and cry1b). Luciferase reporter assays validated the target binding of miR-204-3-3p and miR-430a-3p to the 3'UTRs of cry1a and cry1b, respectively. Furthermore, treatment with mimics and inhibitors of these two miRNAs significantly affected the dynamic expression of their target genes but also other core clock components (clock1a, bmal1b, per1b, per2, per3), as well as the rhythmic locomotor activity of zebrafish larvae. Thus, our identification of light-responsive miRNAs reveals new intricacy in the multi-level regulation of the circadian clockwork by light.
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Affiliation(s)
- Zuo Wang
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
| | - Shuang Wang
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
| | - Yi Bi
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Alessandra Boiti
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Shengxiang Zhang
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
| | - Daniela Vallone
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Nicholas S. Foulkes
- Institute of Biological and Chemical Systems, Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Haiyu Zhao
- School of Life Sciences, Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
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Dobrovinskaya O, Alamilla J, Olivas-Aguirre M. Impact of Modern Lifestyle on Circadian Health and Its Contribution to Adipogenesis and Cancer Risk. Cancers (Basel) 2024; 16:3706. [PMID: 39518143 PMCID: PMC11545514 DOI: 10.3390/cancers16213706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 10/29/2024] [Accepted: 10/30/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND Recent research underscores a crucial connection between circadian rhythm disruption and cancer promotion, highlighting an urgent need for attention. OBJECTIVES Explore the molecular mechanisms by which modern lifestyle factors-such as artificial light exposure, shift work, and dietary patterns-affect cortisol/melatonin regulation and cancer risk. METHODS Employing a narrative review approach, we synthesized findings from Scopus, Google Scholar, and PubMed to analyze lifestyle impacts on circadian health, focusing on cortisol and melatonin chronobiology as molecular markers. We included studies that documented quantitative changes in these markers due to modern lifestyle habits, excluding those lacking quantitative data or presenting inconclusive results. Subsequent sections focused solely on articles that quantified the effects of circadian disruption on adipogenesis and tumor microenvironment modifications. RESULTS This review shows how modern habits lead to molecular changes in cortisol and melatonin, creating adipose microenvironments that support cancer development. These disruptions facilitate immune evasion, chemotherapy resistance, and tumor growth, highlighting the critical roles of cortisol dysregulation and melatonin imbalance. CONCLUSIONS Through the presented findings, we establish a causal link between circadian rhythm dysregulation and the promotion of certain cancer types. By elucidating this relationship, the study emphasizes the importance of addressing lifestyle factors that contribute to circadian misalignment, suggesting that targeted interventions could play a crucial role in mitigating cancer risk and improving overall health outcomes.
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Affiliation(s)
- Oxana Dobrovinskaya
- Laboratory of Immunobiology and Ionic Transport Regulation, University Center for Biomedical Research, University of Colima, Colima 28040, Mexico;
| | - Javier Alamilla
- Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Programa de Investigadores e Investigadoras por México, México City 03940, Mexico;
- Centro Universitario de Investigaciones Biomédicas (CUIB), Universidad de Colima, Colima 28040, Mexico
| | - Miguel Olivas-Aguirre
- Consejo Nacional de Humanidades, Ciencia y Tecnología (CONAHCYT), Programa de Investigadores e Investigadoras por México, México City 03940, Mexico;
- Laboratory of Cancer Pathophysiology, University Center for Biomedical Research, University of Colima, Colima 28040, Mexico
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7
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Uriu K, Hernandez-Sanchez JP, Kojima S. Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms. NPJ Syst Biol Appl 2024; 10:119. [PMID: 39414861 PMCID: PMC11484753 DOI: 10.1038/s41540-024-00451-4] [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] [Received: 06/04/2024] [Accepted: 10/03/2024] [Indexed: 10/18/2024] Open
Abstract
Antisense transcripts are a unique group of non-coding RNAs and play regulatory roles in a variety of biological processes, including circadian rhythms. Per2AS is an antisense transcript to the sense core clock gene Period2 (Per2) in mouse and its expression is rhythmic and antiphasic to Per2. To understand the impact of Per2AS-Per2 interaction, we developed a new mathematical model that mechanistically described the mutually repressive relationship between Per2 and Per2AS. This mutual repression can regulate both amplitude and period of circadian oscillation by affecting a negative feedback regulation of Per2. Simulations from this model also fit with experimental observations that could not be fully explained by our previous model. Our revised model can not only serve as a foundation to build more detailed models to better understand the impact of Per2AS-Per2 interaction in the future, but also be used to analyze other sense-antisense RNA pairs that mutually repress each other.
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Affiliation(s)
- Koichiro Uriu
- School of Life Science and Technology, Institute of Science Tokyo, Meguro, Tokyo, Japan.
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, Japan.
| | - Juan P Hernandez-Sanchez
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA
| | - Shihoko Kojima
- Department of Biological Sciences, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA, USA.
- Center for the Mathematics of Biosystems, Virginia Tech, Blacksburg, VA, USA.
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8
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Swaminathan A, Kenzior A, McCoin C, Price A, Weaver K, Hintermann A, Morris N, Keene AC, Rohner N. A repeatedly evolved mutation in Cryptochrome-1 of subterranean animals alters behavioral and molecular circadian rhythms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613894. [PMID: 39386508 PMCID: PMC11463651 DOI: 10.1101/2024.09.19.613894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
The repeated evolution of similar phenotypes in independent lineages often occurs in response to similar environmental pressures, through similar or different molecular pathways. Recently, a repeatedly occurring mutation R263Q in a conserved domain of the protein Cryptochrome-1 (CRY1) was reported in multiple species inhabiting subterranean environments. Cryptochromes regulate circadian rhythms, and glucose and lipid metabolism. Subterranean species show changes to their circadian rhythm and metabolic pathways, making it likely that this mutation in CRY1 contributes to adaptive phenotypic changes. To identify the functional consequences of the CRY1 R263Q mutation, we generated a mouse model homozygous for this mutation. Indirect calorimetry experiments revealed delayed energy expenditure, locomotor activity and feeding patterns of mutant mice in the dark phase, but no further metabolic phenotypes - unlike a full loss of function of CRY1. Gene expression analyses showed altered expression of several canonical circadian genes in the livers of the mutant mice, fortifying the notion that CRY1 R263Q impacts metabolism. Our data provide the first characterization of a novel mutation that has repeatedly evolved in subterranean environments, supporting the idea that shared environmental constraints can drive the evolution of similar phenotypes through similar genetic changes.
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9
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Hu Y, Oleshko S, Firmani S, Zhu Z, Cheng H, Ulmer M, Arnold M, Colomé-Tatché M, Tang J, Xhonneux S, Marsico A. Path-based reasoning for biomedical knowledge graphs with BioPathNet. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599219. [PMID: 39149355 PMCID: PMC11326122 DOI: 10.1101/2024.06.17.599219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Understanding complex interactions in biomedical networks is crucial for advancements in biomedicine, but traditional link prediction (LP) methods are limited in capturing this complexity. Representation-based learning techniques improve prediction accuracy by mapping nodes to low-dimensional embeddings, yet they often struggle with interpretability and scalability. We present BioPathNet, a novel graph neural network framework based on the Neural Bellman-Ford Network (NBFNet), addressing these limitations through path-based reasoning for LP in biomedical knowledge graphs. Unlike node-embedding frameworks, BioPathNet learns representations between node pairs by considering all relations along paths, enhancing prediction accuracy and interpretability. This allows visualization of influential paths and facilitates biological validation. BioPathNet leverages a background regulatory graph (BRG) for enhanced message passing and uses stringent negative sampling to improve precision. In evaluations across various LP tasks, such as gene function annotation, drug-disease indication, synthetic lethality, and lncRNA-mRNA interaction prediction, BioPathNet consistently outperformed shallow node embedding methods, relational graph neural networks and task-specific state-of-the-art methods, demonstrating robust performance and versatility. Our study predicts novel drug indications for diseases like acute lymphoblastic leukemia (ALL) and Alzheimer's, validated by medical experts and clinical trials. We also identified new synthetic lethality gene pairs and regulatory interactions involving lncRNAs and target genes, confirmed through literature reviews. BioPathNet's interpretability will enable researchers to trace prediction paths and gain molecular insights, making it a valuable tool for drug discovery, personalized medicine and biology in general.
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Affiliation(s)
- Yue Hu
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
| | - Svitlana Oleshko
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Computation, Information and Technology, Technical University of Munich, Arcisstrasse 21, Munich, 80333, Bavaria, Germany
| | - Samuele Firmani
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
| | - Zhaocheng Zhu
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Quebec, Canada
| | - Hui Cheng
- School of Computation, Information and Technology, Technical University of Munich, Arcisstrasse 21, Munich, 80333, Bavaria, Germany
| | - Maria Ulmer
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
| | - Matthias Arnold
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- Department of Psychiatry and Behavioural Sciences, Duke University, 905 W Main St., Durham, NC 27701, North Carolina, United States
| | - Maria Colomé-Tatché
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
- School of Life Sciences, Technical University of Munich, Alte Akademie 8, Freising, 85354, Bavaria, Germany
- Faculty of Biology, Ludwig-Maximilian University of Munich, Grosshaderner Str. 2, Planegg-Martinsried, 82152, Bavaria, Germany
| | - Jian Tang
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, CIFAR AI Chair, 661 University Ave, Toronto, ON M5G 1M1, Ontario, Canada
- Department, HEC Montréal, 3000 Chem. de la Côte-Sainte-Catherine, Montréal, QC H3T 2A7, Quebec, Canada
| | - Sophie Xhonneux
- Department, Mila - Québec AI Institute, 6666 St-Urbain, Montréal, QC H2S 3H1, Quebec, Canada
- Department, Université de Montréal, 2900, boul. Édouard-Montpetit, Montréal, QC H3T 1J4, Quebec, Canada
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Ingolstaedter Landstrasse 1, Neuherberg, 85764, Bavaria, Germany
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10
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Ryabov NA, Volova LT, Alekseev DG, Kovaleva SA, Medvedeva TN, Vlasov MY. Mass Spectrometry of Collagen-Containing Allogeneic Human Bone Tissue Material. Polymers (Basel) 2024; 16:1895. [PMID: 39000751 PMCID: PMC11244277 DOI: 10.3390/polym16131895] [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: 04/08/2024] [Revised: 06/02/2024] [Accepted: 06/07/2024] [Indexed: 07/17/2024] Open
Abstract
The current paper highlights the active development of tissue engineering in the field of the biofabrication of living tissue analogues through 3D-bioprinting technology. The implementation of the latter is impossible without important products such as bioinks and their basic components, namely, hydrogels. In this regard, tissue engineers are searching for biomaterials to produce hydrogels with specified properties both in terms of their physical, mechanical and chemical properties and in terms of local biological effects following implantation into an organism. One of such effects is the provision of the optimal conditions for physiological reparative regeneration by the structural components that form the basis of the biomaterial. Therefore, qualitative assessment of the composition of the protein component of a biomaterial is a significant task in tissue engineering and bioprinting. It is important for predicting the behaviour of printed constructs in terms of their gradual resorption followed by tissue regeneration due to the formation of a new extracellular matrix. One of the most promising natural biomaterials with significant potential in the production of hydrogels and the bioinks based on them is the polymer collagen of allogeneic origin, which plays an important role in maintaining the structural and biological integrity of the extracellular matrix, as well as in the morphogenesis and cellular metabolism of tissues, giving them the required mechanical and biochemical properties. In tissue engineering, collagen is widely used as a basic biomaterial because of its availability, biocompatibility and facile combination with other materials. This manuscript presents the main results of a mass spectrometry analysis (proteomic assay) of the lyophilized hydrogel produced from the registered Lyoplast® bioimplant (allogeneic human bone tissue), which is promising in the field of biotechnology. Proteomic assays of the investigated lyophilized hydrogel sample showed the presence of structural proteins (six major collagen fibers of types I, II, IV, IX, XXVII, XXVIII were identified), extracellular matrix proteins, and mRNA-stabilizing proteins, which participate in the regulation of transcription, as well as inducer proteins that mediate the activation of regeneration, including the level of circadian rhythm. The research results offer a new perspective and indicate the significant potential of the lyophilized hydrogels as an effective alternative to synthetic and xenogeneic materials in regenerative medicine, particularly in the field of biotechnology, acting as a matrix and cell-containing component of bioinks for 3D bioprinting.
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Affiliation(s)
- Nikolay A. Ryabov
- Research Institute of Biotechnology “BioTech”, Samara State Medical University of the Ministry of Health of the Russian Federation, 443079 Samara, Russia; (N.A.R.); (L.T.V.); (M.Y.V.)
| | - Larisa T. Volova
- Research Institute of Biotechnology “BioTech”, Samara State Medical University of the Ministry of Health of the Russian Federation, 443079 Samara, Russia; (N.A.R.); (L.T.V.); (M.Y.V.)
| | - Denis G. Alekseev
- Research Institute of Biotechnology “BioTech”, Samara State Medical University of the Ministry of Health of the Russian Federation, 443079 Samara, Russia; (N.A.R.); (L.T.V.); (M.Y.V.)
| | - Svetlana A. Kovaleva
- Core Shared Research Facility “Industrial Biotechnologies”, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 117312 Moscow, Russia;
| | - Tatyana N. Medvedeva
- Research Institute of Biotechnology “BioTech”, Samara State Medical University of the Ministry of Health of the Russian Federation, 443079 Samara, Russia; (N.A.R.); (L.T.V.); (M.Y.V.)
| | - Mikhail Yu. Vlasov
- Research Institute of Biotechnology “BioTech”, Samara State Medical University of the Ministry of Health of the Russian Federation, 443079 Samara, Russia; (N.A.R.); (L.T.V.); (M.Y.V.)
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11
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Yamaguchi Y. Arginine vasopressin: Critical regulator of circadian homeostasis. Peptides 2024; 177:171229. [PMID: 38663583 DOI: 10.1016/j.peptides.2024.171229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Circadian rhythms optimally regulate numerous physiological processes in an organism and synchronize them with the external environment. The suprachiasmatic nucleus (SCN), the center of the circadian clock in mammals, is composed of multiple cell types that form a network that provides the basis for the remarkable stability of the circadian clock. Among the neuropeptides expressed in the SCN, arginine vasopressin (AVP) has attracted much attention because of its deep involvement in the function of circadian rhythms, as elucidated in particular by studies using genetically engineered mice. This review briefly summarizes the current knowledge on the peptidergic distribution and topographic neuronal organization in the SCN, the molecular mechanisms of the clock genes, and the relationship between the SCN and peripheral clocks. With respect to the physiological roles of AVP and AVP-expressing neurons, in addition to a sex-dependent action of AVP in the SCN, studies using AVP receptor knockout mice and mice genetically manipulated to alter the clock properties of AVP neurons are summarized here, highlighting its importance in maintaining circadian homeostasis and its potential as a target for therapeutic interventions.
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Affiliation(s)
- Yoshiaki Yamaguchi
- Department of Life Science and Biotechnology, Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Japan.
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12
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Touitou Y, Cermakian N, Touitou C. The environment and the internal clocks: The study of their relationships from prehistoric to modern times. Chronobiol Int 2024; 41:859-887. [PMID: 38757600 DOI: 10.1080/07420528.2024.2353857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/17/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
The origin of biological rhythms goes back to the very beginning of life. They are observed in the animal and plant world at all levels of organization, from cells to ecosystems. As early as the 18th century, plant scientists were the first to explain the relationship between flowering cycles and environmental cycles, emphasizing the importance of daily light-dark cycles and the seasons. Our temporal structure is controlled by external and internal rhythmic signals. Light is the main synchronizer of the circadian system, as daily exposure to light entrains our clock over 24 hours, the endogenous period of the circadian system being close to, but not exactly, 24 hours. In 1960, a seminal scientific meeting, the Cold Spring Harbor Symposium on Biological Rhythms, brought together all the biological rhythms scientists of the time, a number of whom are considered the founders of modern chronobiology. All aspects of biological rhythms were addressed, from the properties of circadian rhythms to their practical and ecological aspects. Birth of chronobiology dates from this period, with the definition of its vocabulary and specificities in metabolism, photoperiodism, animal physiology, etc. At around the same time, and right up to the present day, research has focused on melatonin, the circadian neurohormone of the pineal gland, with data on its pattern, metabolism, control by light and clinical applications. However, light has a double face, as it has positive effects as a circadian clock entraining agent, but also deleterious effects, as it can lead to chronodisruption when exposed chronically at night, which can increase the risk of cancer and other diseases. Finally, research over the past few decades has unraveled the anatomical location of circadian clocks and their cellular and molecular mechanisms. This recent research has in turn allowed us to explain how circadian rhythms control physiology and health.
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Affiliation(s)
- Yvan Touitou
- Unité de Chronobiologie, Fondation A. de Rothschild, Paris, France
| | - Nicolas Cermakian
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec, Canada
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13
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Avila A, Zhang SL. A circadian clock regulates the blood-brain barrier across phylogeny. VITAMINS AND HORMONES 2024; 126:241-287. [PMID: 39029975 DOI: 10.1016/bs.vh.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/21/2024]
Abstract
As the central regulatory system of an organism, the brain is responsible for overseeing a wide variety of physiological processes essential for an organism's survival. To maintain the environment necessary for neurons to function, the brain requires highly selective uptake and elimination of specific molecules through the blood-brain barrier (BBB). As an organism's activities vary throughout the day, how does the BBB adapt to meet the changing needs of the brain? A mechanism is through temporal regulation of BBB permeability via its circadian clock, which will be the focal point of this chapter. To comprehend the circadian clock's role within the BBB, we will first examine the anatomy of the BBB and the transport mechanisms enabling it to fulfill its role as a restrictive barrier. Next, we will define the circadian clock, and the discussion will encompass an introduction to circadian rhythms, the Transcription-Translation Feedback Loop (TTFL) as the mechanistic basis of circadian timekeeping, and the organization of tissue clocks found in organisms. Then, we will cover the role of the circadian rhythms in regulating the cellular mechanisms and functions of the BBB. We discuss the implications of this regulation in influencing sleep behavior, the progression of neurodegenerative diseases, and finally drug delivery for treatment of neurological diseases.
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Affiliation(s)
- Ashley Avila
- Cell Biology Department, Emory University, Atlanta, GA, United States
| | - Shirley L Zhang
- Cell Biology Department, Emory University, Atlanta, GA, United States.
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14
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Uriu K, Hernandez-Sanchez JP, Kojima S. Impacts of the feedback loop between sense-antisense RNAs in regulating circadian rhythms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591560. [PMID: 38746188 PMCID: PMC11092440 DOI: 10.1101/2024.04.28.591560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Antisense transcripts are a unique group of non-coding RNAs that are transcribed from the opposite strand of a sense coding gene in an antisense orientation. Even though they do not encode a protein, these transcripts play a regulatory role in a variety of biological processes, including circadian rhythms. We and others found an antisense transcript, Per2AS , that is transcribed from the strand opposite the sense transcript Period2 ( Per2 ) and exhibits a rhythmic and antiphasic expression pattern compared to Per2 in mouse. By assuming that Per2AS and Per2 mutually repress each other, our previous mathematical model predicted that Per2AS regulates the robustness and the amplitude of circadian rhythms. In this study, we revised our previous model and developed a new mathematical model that mechanistically described the mutually repressive relationship between Per2 and Per2AS via transcriptional interference. We found that the simulation results are largely consistent with experimental observations including the counterintuitive ones that could not be fully explained by our previous model. These results indicate that our revised model serves as a foundation to build more detailed models in the future to better understand the impact of Per2AS-Per2 interaction in the mammalian circadian clock. Our mechanistic description of Per2AS-Per2 interaction can also be extended to other mathematical models that involve sense-antisense RNA pairs that mutually repress each other.
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15
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Li T, Jiang Y, Bai Y, Jiang K, Du G, Chen P, Luo C, Li L, Qiao J, Shen J. A review for the impacts of circadian disturbance on urological cancers. Sleep Biol Rhythms 2024; 22:163-180. [PMID: 38524168 PMCID: PMC10959858 DOI: 10.1007/s41105-023-00500-1] [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: 06/29/2023] [Accepted: 10/18/2023] [Indexed: 03/26/2024]
Abstract
Circadian rhythm is an internal timing system and harmonizes a variety of cellular, behavioral, and physiological processes to daily environment. Circadian disturbance caused by altered life style or disrupted sleep patterns inevitably contributes to various disorders. As the rapidly increased cancer occurrences and subsequent tremendous financial burdens, more researches focus on reducing the morbidity rather than treating it. Recently, many epidemiologic studies demonstrated that circadian disturbance was tightly related to the occurrence and development of cancers. For urinary system, numerous clinical researches observed the incidence and progress of prostate cancer were influenced by nightshift work, sleep duration, chronotypes, light exposure, and meal timing, this was also proved by many genetic and fundamental findings. Although the epidemiological studies regarding the relationship between circadian disturbance and kidney/bladder cancers were relative limited, some basic researches still claimed circadian disruption was closely correlated to these two cancers. The role of circadian chemotherapy on cancers of prostate, kidney, and bladder were also explored, however, it has not been regularly recommended considering the limited evidence and poor standard protocols. Finally, the researches for the impacts of circadian disturbance on cancers of adrenal gland, penis, testis were not found at present. In general, a better understanding the relationship between circadian disturbance and urological cancers might help to provide more scientific work schedules and rational lifestyles which finally saving health resource by reducing urological tumorigenesis, however, the underlying mechanisms are complex which need further exploration.
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Affiliation(s)
- Tao Li
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yiting Jiang
- Department of Otorhinolaryngology, The Ninth People’s Hospital of Chongqing, Chongqing, China
| | - Yunjin Bai
- Department of Urology and Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Kehua Jiang
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Guangshi Du
- Translational Medicine Research Center of Guizhou Medical University, Guiyang, China
| | - Peng Chen
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Chao Luo
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Lei Li
- Gastrointestinal Surgery Center, School of Medicine, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Qiao
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jun Shen
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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16
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Yajima K, Chiba S, Park I, Ogata H, Kayaba M, Ishihara A, Tanaka Y, Simeng Z, Jaehoon S, Katakura M, Tokuyama K. Dietary palmitic acid to oleic acid ratio modulates energy metabolism and biological rhythms in young healthy Japanese males. Br J Nutr 2024; 131:447-460. [PMID: 37578022 DOI: 10.1017/s0007114523001770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The present study investigated the potential role of the composition of dietary fatty acids in the regulation of biological rhythms, such as the sleep architecture, core body temperature and leukocyte clock gene expression, in subjects fed meals rich in palmitic acid (PA) or oleic acid (OA). Eleven males participated in two sessions of indirect calorimetry in a whole-room metabolic chamber. In each session, subjects consumed three meals rich in PA (44·3 % of total fat as PA and 42·3 % as OA) or OA (11·7 % of total fat as PA and 59·3 % as OA) in the metabolic chamber. The ratio of PA to OA in plasma was significantly lower and fat oxidation was significantly higher during 24 h of indirect calorimetry in the session with meals rich in OA than in that with meals rich in PA. The duration of slow wave sleep (SWS) was shorter, the latency of SWS was longer and the nadir of core body temperature after bedtime was later in the session with meals rich in PA than in that with meals rich in OA. The peak in CRY1 gene expression was earlier and its amplitude was higher in the session with meals rich in PA than in that with meals rich in OA. In healthy young males, meals rich in PA decreased fat oxidation and disrupted biological rhythms, particularly the sleep architecture and core body temperature during sleep, more than meals rich in OA.
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Affiliation(s)
- Katsuhiko Yajima
- Laboratory of Nutritional Physiology, Faculty of Pharmaceutical Sciences, Josai University, Saitama, Japan
| | - Shuto Chiba
- Laboratory of Nutritional Physiology, Faculty of Pharmaceutical Sciences, Josai University, Saitama, Japan
| | - Insung Park
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hitomi Ogata
- Graduate School of Humanities and Social Sciences, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Momoko Kayaba
- Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Asuka Ishihara
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiaki Tanaka
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Zhang Simeng
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Seol Jaehoon
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
- Research Center for Overwork-Related Disorders, National Institute of Occupational Safety and Health, Japan (JNIOSH), Kanagawa, Japan
- R&D Center for Tailor-Made QOL, University of Tsukuba, Tsukuba, Japan
| | - Masanori Katakura
- Laboratory of Nutritional Physiology, Faculty of Pharmaceutical Sciences, Josai University, Saitama, Japan
| | - Kumpei Tokuyama
- International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
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17
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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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18
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Swaminathan A, Xia F, Rohner N. From darkness to discovery: evolutionary, adaptive, and translational genetic insights from cavefish. Trends Genet 2024; 40:24-38. [PMID: 38707509 PMCID: PMC11068324 DOI: 10.1016/j.tig.2023.10.002] [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: 07/05/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 05/07/2024]
Abstract
How genotype determines phenotype is a well-explored question, but genotype-environment interactions and their heritable impact on phenotype over the course of evolution are not as thoroughly investigated. The fish Astyanax mexicanus, consisting of surface and cave ecotypes, is an ideal emerging model to study the genetic basis of adaptation to new environments. This model has permitted quantitative trait locus mapping and whole-genome comparisons to identify the genetic bases of traits such as albinism and insulin resistance and has helped to better understand fundamental evolutionary mechanisms. In this review, we summarize recent advances in A. mexicanus genetics and discuss their broader impact on the fields of adaptation and evolutionary genetics.
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Affiliation(s)
| | - Fanning Xia
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, MO, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS, USA
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19
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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: 0.5] [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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20
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Nakazato R, Matsuda Y, Ijaz F, Ikegami K. Circadian oscillation in primary cilium length by clock genes regulates fibroblast cell migration. EMBO Rep 2023; 24:e56870. [PMID: 37971148 DOI: 10.15252/embr.202356870] [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: 01/24/2023] [Revised: 08/30/2023] [Accepted: 10/20/2023] [Indexed: 11/19/2023] Open
Abstract
Various mammalian cells have autonomous cellular clocks that are produced by the transcriptional cycle of clock genes. Cellular clocks provide circadian rhythms for cellular functions via transcriptional and cytoskeletal regulation. The vast majority of mammalian cells possess a primary cilium, an organelle protruding from the cell surface. Here, we investigated the little-known relationship between circadian rhythm and primary cilia. The length and number of primary cilia showed circadian dynamics both in vitro and in vivo. The circadian rhythm of primary cilium length was abolished by SR9011 and Bmal1 knockout. A centrosomal protein, pericentrin, transiently accumulates in centriolar satellites, the base of primary cilia at the shortest cilia phase, and induces elongation of primary cilia at the longest cilia phase in the circadian rhythm of primary cilia. In addition, rhythmic cell migration during wound healing depends on the length of primary cilia and affects the rate of wound healing. Our findings demonstrate that the circadian dynamics of primary cilium length by clock genes control fibroblast migration and could provide new insights into chronobiology.
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Affiliation(s)
- Ryota Nakazato
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuki Matsuda
- Hiroshima University School of Medicine, Hiroshima, Japan
| | - Faryal Ijaz
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Koji Ikegami
- Department of Anatomy and Developmental Biology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Kawaguchi, Japan
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21
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McElroy KE, Audino JA, Serb JM. Molluscan Genomes Reveal Extensive Differences in Photopigment Evolution Across the Phylum. Mol Biol Evol 2023; 40:msad263. [PMID: 38039155 PMCID: PMC10733189 DOI: 10.1093/molbev/msad263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/14/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
In animals, opsins and cryptochromes are major protein families that transduce light signals when bound to light-absorbing chromophores. Opsins are involved in various light-dependent processes, like vision, and have been co-opted for light-independent sensory modalities. Cryptochromes are important photoreceptors in animals, generally regulating circadian rhythm, they belong to a larger protein family with photolyases, which repair UV-induced DNA damage. Mollusks are great animals to explore questions about light sensing as eyes have evolved multiple times across, and within, taxonomic classes. We used molluscan genome assemblies from 80 species to predict protein sequences and examine gene family evolution using phylogenetic approaches. We found extensive opsin family expansion and contraction, particularly in bivalve xenopsins and gastropod Go-opsins, while other opsins, like retinochrome, rarely duplicate. Bivalve and gastropod lineages exhibit fluctuations in opsin repertoire, with cephalopods having the fewest number of opsins and loss of at least 2 major opsin types. Interestingly, opsin expansions are not limited to eyed species, and the highest opsin content was seen in eyeless bivalves. The dynamic nature of opsin evolution is quite contrary to the general lack of diversification in mollusk cryptochromes, though some taxa, including cephalopods and terrestrial gastropods, have reduced repertoires of both protein families. We also found complete loss of opsins and cryptochromes in multiple, but not all, deep-sea species. These results help set the stage for connecting genomic changes, including opsin family expansion and contraction, with differences in environmental, and biological features across Mollusca.
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Affiliation(s)
- Kyle E McElroy
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Jorge A Audino
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Zoology, University of São Paulo, São Paulo, Brazil
| | - Jeanne M Serb
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
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22
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Bellfy L, Smies CW, Bernhardt AR, Bodinayake KK, Sebastian A, Stuart EM, Wright DS, Lo CY, Murakami S, Boyd HM, von Abo MJ, Albert I, Kwapis JL. The clock gene Per1 may exert diurnal control over hippocampal memory consolidation. Neuropsychopharmacology 2023; 48:1789-1797. [PMID: 37264172 PMCID: PMC10579262 DOI: 10.1038/s41386-023-01616-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/03/2023]
Abstract
The circadian system influences many different biological processes, including memory performance. While the suprachiasmatic nucleus (SCN) functions as the brain's central pacemaker, downstream "satellite clocks" may also regulate local functions based on the time of day. Within the dorsal hippocampus (DH), for example, local molecular oscillations may contribute to time-of-day effects on memory. Here, we used the hippocampus-dependent Object Location Memory task to determine how memory is regulated across the day/night cycle in mice. First, we systematically determined which phase of memory (acquisition, consolidation, or retrieval) is modulated across the 24 h day. We found that mice show better long-term memory performance during the day than at night, an effect that was specifically attributed to diurnal changes in memory consolidation, as neither memory acquisition nor memory retrieval fluctuated across the day/night cycle. Using RNA-sequencing we identified the circadian clock gene Period1 (Per1) as a key mechanism capable of supporting this diurnal fluctuation in memory consolidation, as learning-induced Per1 oscillates in tandem with memory performance in the hippocampus. We then show that local knockdown of Per1 within the DH impairs spatial memory without affecting either the circadian rhythm or sleep behavior. Thus, Per1 may independently function within the DH to regulate memory in addition to its known role in regulating the circadian system within the SCN. Per1 may therefore exert local diurnal control over memory consolidation within the DH.
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Affiliation(s)
- Lauren Bellfy
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Chad W Smies
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Alicia R Bernhardt
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Kasuni K Bodinayake
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Aswathy Sebastian
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Emily M Stuart
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Destiny S Wright
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Chen-Yu Lo
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Shoko Murakami
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Hannah M Boyd
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Megan J von Abo
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Istvan Albert
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Janine L Kwapis
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
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23
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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: 1] [Impact Index Per Article: 0.5] [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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24
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Li W, Xiong X, Kiperman T, Ma K. Transcription Repression of CRY2 via PER2 Interaction Promotes Adipogenesis. Mol Cell Biol 2023; 43:500-514. [PMID: 37724597 PMCID: PMC10569361 DOI: 10.1080/10985549.2023.2253710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
The circadian clock is driven by a transcriptional-translational feedback loop, and cryptochrome 2 (CRY2) represses CLOCK/BMAL1-induced transcription activation. Despite the established role of clock in adipogenic regulation, whether the CRY2 repressor activity functions in adipocyte biology remains unclear. Here we identify a critical cysteine residue of CRY2 that mediates interaction with Period 2 (PER2). We further demonstrate that this mechanism is required for repressing circadian clock-controlled Wnt signaling to promote adipogenesis. CRY2 protein is enriched in white adipose depots and robustly induced by adipogenic differentiation. Via site-directed mutagenesis, we identified that a conserved CRY2 cysteine at 432 within the loop interfacing with PER2 mediates heterodimer complex formation that confers transcription repression. C432 mutation disrupted PER2 association without affecting BMAL1 binding, leading to loss of repression of clock transcription activation. In preadipocytes, whereas CRY2 enhanced adipocyte differentiation, the repression-defective C432 mutant suppressed this process. Furthermore, silencing of CRY2 attenuated, while stabilization of CRY2 by KL001 markedly augmented adipocyte maturation. Mechanistically, we show that transcriptional repression of Wnt pathway components underlies CRY2 modulation of adipogenesis. Collectively, our findings elucidate a CRY2-mediated repression mechanism that promotes adipocyte development, and implicate its potential as a clock intervention target for obesity.
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Affiliation(s)
- Weini Li
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Xuekai Xiong
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Tali Kiperman
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Ke Ma
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
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25
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Zhang L, Malkemper EP. Cryptochromes in mammals: a magnetoreception misconception? Front Physiol 2023; 14:1250798. [PMID: 37670767 PMCID: PMC10475740 DOI: 10.3389/fphys.2023.1250798] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
Cryptochromes are flavoproteins related to photolyases that are widespread throughout the plant and animal kingdom. They govern blue light-dependent growth in plants, control circadian rhythms in a light-dependent manner in invertebrates, and play a central part in the circadian clock in vertebrates. In addition, cryptochromes might function as receptors that allow animals to sense the Earth's magnetic field. As cryptochromes are also present in mammals including humans, the possibility of a magnetosensitive protein is exciting. Here we attempt to provide a concise overview of cryptochromes in mammals. We briefly review their canonical role in the circadian rhythm from the molecular level to physiology, behaviour and diseases. We then discuss their disputed light sensitivity and proposed role in the magnetic sense in mammals, providing three mechanistic hypotheses. Specifically, mammalian cryptochromes could form light-induced radical pairs in particular cellular milieus, act as magnetoreceptors in darkness, or as secondary players in a magnetoreception signalling cascade. Future research can test these hypotheses to investigate if the role of mammalian cryptochromes extends beyond the circadian clock.
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Affiliation(s)
| | - E. Pascal Malkemper
- Max Planck Research Group Neurobiology of Magnetoreception, Max Planck Institute for Neurobiology of Behavior—caesar, Bonn, Germany
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26
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Sato S, Hishida T, Kinouchi K, Hatanaka F, Li Y, Nguyen Q, Chen Y, Wang PH, Kessenbrock K, Li W, Izpisua Belmonte JC, Sassone-Corsi P. The circadian clock CRY1 regulates pluripotent stem cell identity and somatic cell reprogramming. Cell Rep 2023; 42:112590. [PMID: 37261952 DOI: 10.1016/j.celrep.2023.112590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Distinct metabolic conditions rewire circadian-clock-controlled signaling pathways leading to the de novo construction of signal transduction networks. However, it remains unclear whether metabolic hallmarks unique to pluripotent stem cells (PSCs) are connected to clock functions. Reprogramming somatic cells to a pluripotent state, here we highlighted non-canonical functions of the circadian repressor CRY1 specific to PSCs. Metabolic reprogramming, including AMPK inactivation and SREBP1 activation, was coupled with the accumulation of CRY1 in PSCs. Functional assays verified that CRY1 is required for the maintenance of self-renewal capacity, colony organization, and metabolic signatures. Genome-wide occupancy of CRY1 identified CRY1-regulatory genes enriched in development and differentiation in PSCs, albeit not somatic cells. Last, cells lacking CRY1 exhibit differential gene expression profiles during induced PSC (iPSC) reprogramming, resulting in impaired iPSC reprogramming efficiency. Collectively, these results suggest the functional implication of CRY1 in pluripotent reprogramming and ontogenesis, thereby dictating PSC identity.
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Affiliation(s)
- Shogo Sato
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA; Center for Biological Clocks Research, Department of Biology, Texas A&M University, College Station, TX, USA.
| | - Tomoaki Hishida
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Laboratory of Biological Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, Wakayama, Japan
| | - Kenichiro Kinouchi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Fumiaki Hatanaka
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA
| | - Yumei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Quy Nguyen
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Yumay Chen
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Ping H Wang
- UC Irvine Diabetes Center, Sue and Bill Gross Stem Cell Research Center, Department of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Kai Kessenbrock
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Wei Li
- Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Juan Carlos Izpisua Belmonte
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Altos Labs, San Diego, CA, USA.
| | - Paolo Sassone-Corsi
- Center for Epigenetics and Metabolism, Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, CA, USA
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27
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Schirmer AE, Kumar V, Schook A, Song EJ, Marshall MS, Takahashi JS. Cry1 expression during postnatal development is critical for the establishment of normal circadian period. Front Neurosci 2023; 17:1166137. [PMID: 37389366 PMCID: PMC10300422 DOI: 10.3389/fnins.2023.1166137] [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: 02/14/2023] [Accepted: 05/23/2023] [Indexed: 07/01/2023] Open
Abstract
The mammalian circadian system generates an approximate 24-h rhythm through a complex autoregulatory feedback loop. Four genes, Period1 (Per1), Period2 (Per2), Cryptochrome1 (Cry1), and Cryptochrome2 (Cry2), regulate the negative feedback within this loop. Although these proteins have distinct roles within the core circadian mechanism, their individual functions are poorly understood. Here, we used a tetracycline trans-activator system (tTA) to examine the role of transcriptional oscillations in Cry1 and Cry2 in the persistence of circadian activity rhythms. We demonstrate that rhythmic Cry1 expression is an important regulator of circadian period. We then define a critical period from birth to postnatal day 45 (PN45) where the level of Cry1 expression is critical for setting the endogenous free running period in the adult animal. Moreover, we show that, although rhythmic Cry1 expression is important, in animals with disrupted circadian rhythms overexpression of Cry1 is sufficient to restore normal behavioral periodicity. These findings provide new insights into the roles of the Cryptochrome proteins in circadian rhythmicity and further our understanding of the mammalian circadian clock.
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Affiliation(s)
- Aaron E. Schirmer
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- Department of Biology, Northeastern Illinois University, Chicago, IL, United States
| | - Vivek Kumar
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Andrew Schook
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
| | - Eun Joo Song
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
| | - Michael S. Marshall
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Joseph S. Takahashi
- Department of Neurobiology, Northwestern University, Evanston, IL, United States
- Department of Neuroscience, Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
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28
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Kwiatkowski ER, Schnytzer Y, Rosenthal JJC, Emery P. Behavioral circatidal rhythms require Bmal1 in Parhyale hawaiensis. Curr Biol 2023; 33:1867-1882.e5. [PMID: 36977416 PMCID: PMC10205697 DOI: 10.1016/j.cub.2023.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/20/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023]
Abstract
Organisms living in the intertidal zone are exposed to a particularly challenging environment. In addition to daily changes in light intensity and seasonal changes in photoperiod and weather patterns, they experience dramatic oscillations in environmental conditions due to the tides. To anticipate tides, and thus optimize their behavior and physiology, animals occupying intertidal ecological niches have acquired circatidal clocks. Although the existence of these clocks has long been known, their underlying molecular components have proven difficult to identify, in large part because of the lack of an intertidal model organism amenable to genetic manipulation. In particular, the relationship between the circatidal and circadian molecular clocks, and the possibility of shared genetic components, has been a long-standing question. Here, we introduce the genetically tractable crustacean Parhyale hawaiensis as a system for the study of circatidal rhythms. First, we show that P. hawaiensis exhibits robust 12.4-h rhythms of locomotion that can be entrained to an artificial tidal regimen and are temperature compensated. Using CRISPR-Cas9 genome editing, we then demonstrate that the core circadian clock gene Bmal1 is required for circatidal rhythms. Our results thus demonstrate that Bmal1 is a molecular link between circatidal and circadian clocks and establish P. hawaiensis as a powerful system to study the molecular mechanisms underlying circatidal rhythms and their entrainment.
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Affiliation(s)
- Erica R Kwiatkowski
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Yisrael Schnytzer
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar-Ilan University, Ramat Gan 5290002, Israel; The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Joshua J C Rosenthal
- The Eugene Bell Center, The Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Patrick Emery
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA.
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29
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Amidfar M, Garcez ML, Kim YK. The shared molecular mechanisms underlying aging of the brain, major depressive disorder, and Alzheimer's disease: The role of circadian rhythm disturbances. Prog Neuropsychopharmacol Biol Psychiatry 2023; 123:110721. [PMID: 36702452 DOI: 10.1016/j.pnpbp.2023.110721] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/07/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
An association with circadian clock function and pathophysiology of aging, major depressive disorder (MDD), and Alzheimer's disease (AD) is well established and has been proposed as a factor in the development of these diseases. Depression and changes in circadian rhythm have been increasingly suggested as the two primary overlapping and interpenetrating changes that occur with aging. The relationship between AD and depression in late life is not completely understood and probably is complex. Patients with major depression or AD suffer from disturbed sleep/wake cycles and altered rhythms in daily activities. Although classical monoaminergic hypotheses are traditionally proposed to explain the pathophysiology of MDD, several clinical and preclinical studies have reported a strong association between circadian rhythm and mood regulation. In addition, a large body of evidence supports an association between disruption of circadian rhythm and AD. Some clock genes are dysregulated in rodent models of depression. If aging, AD, and MDD share a common biological basis in pathophysiology, common therapeutic tools could be investigated for their prevention and treatment. Nitro-oxidative stress (NOS), for example, plays a fundamental role in aging, as well as in the pathogenesis of AD and MDD and is associated with circadian clock disturbances. Thus, development of therapeutic possibilities with these NOS-related conditions is advisable. This review describes recent findings that link disrupted circadian clocks to aging, MDD, and AD and summarizes the experimental evidence that supports connections between the circadian clock and molecular pathologic factors as shared common pathophysiological mechanisms underlying aging, AD, and MDD.
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Affiliation(s)
- Meysam Amidfar
- Department of Neuroscience, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Michelle Lima Garcez
- Laboratory of Translational Neuroscience, Department of Biochemistry, Federal University of Santa Catarina (UFSC), Florianópolis, Santa Catarina, Brazil
| | - Yong-Ku Kim
- Department of Psychiatry, College of Medicine, Korea University, Seoul, South Korea.
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30
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Tice AL, Laudato JA, Gordon BS, Steiner JL. Chronic Alcohol Consumption Disrupts the Skeletal Muscle Circadian Clock in Female Mice. J Biol Rhythms 2023; 38:159-170. [PMID: 36579773 DOI: 10.1177/07487304221141464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The intrinsic skeletal muscle core clock has emerged as a key feature of metabolic control and influences several aspects of muscle physiology. Acute alcohol intoxication disrupts the core molecular clock, but whether chronic consumption, like that leading to alcoholic myopathy, is also a zeitgeber for skeletal muscle remains unknown. The purpose of this work was to determine whether chronic alcohol consumption dysregulates the skeletal muscle core molecular clock and clock-controlled genes (CCGs). C57BL/6Hsd female mice (14 weeks old) were fed a control (CON) or alcohol (EtOH) containing liquid diet for 6 weeks. Gastrocnemius muscles and serum were collected from CON and EtOH mice every 4-h for 24-h. Chronic alcohol consumption disrupted genes of the core clock including suppressing the rhythmic peak of expression of Bmal1, Per1, Per2, and Cry2. Genes involved in the regulation of Bmal1 also exhibited lower rhythmic peaks including Reverb α and Myod1. The CCGs, Dbp, Lpl, Hk2, and Hadh were also suppressed by alcohol. The nuclear expression patterns of MYOD1, DBP, and REVERBα were shifted by alcohol, while no change in BMAL1 was detected. Overall, these data indicate that alcohol disrupted the skeletal muscle core clock but whether these changes in the core clock are causative or a consequence of alcoholic myopathy requires future mechanistic confirmation.
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Affiliation(s)
- Abigail L Tice
- Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, Florida
| | - Joseph A Laudato
- Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, Florida
| | - Bradley S Gordon
- Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, Florida
- Institute of Sports Sciences and Medicine, Florida State University, Tallahassee, Florida
| | - Jennifer L Steiner
- Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, Florida
- Institute of Sports Sciences and Medicine, Florida State University, Tallahassee, Florida
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31
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Otsuka K, Cornelissen G, Weydahl A, Gubin D, Beaty LA, Murase M. Rules of Heliogeomagnetics Diversely Coordinating Biological Rhythms and Promoting Human Health. APPLIED SCIENCES 2023; 13:951. [DOI: 10.3390/app13020951] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Abstract
This investigation reviews how geomagnetic activity affects the circadian variation in blood pressure (BP) and heart rate (HR) and their variabilities of clinically healthy individuals. A small study in Alta, Norway (latitude of 70.0° N), serves to illustrate the methodology used to outline rules of procedure in exploring heliogeomagnetic effects on human physiology. Volunteers in the Alta study were monitored for at least 2 days between 18 March 2002 and 9 January 2005. Estimates of the circadian characteristics of BP and HR by cosinor and the Maximum Entropy Method (MEM) indicate an increase in the circadian amplitude of systolic (S) BP on geomagnetic-disturbance days compared to quiet days (p = 0.0236). Geomagnetic stimulation was found to be circadian-phase dependent, with stimulation in the evening inducing a 49.2% increase in the circadian amplitude of SBP (p = 0.0003), not observed in relation to stimulation in the morning. In two participants monitored for 7 days, the circadian amplitude of SBP decreased by 23.4% on an extremely disturbed day but increased by 50.3% on moderately disturbed days (p = 0.0044), suggesting a biphasic (hormetic) reaction of the circadian SBP rhythm to geomagnetics. These results indicate a possible role of geomagnetic fluctuations in modulating the circadian system.
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Affiliation(s)
- Kuniaki Otsuka
- Tokyo Women’s Medical University, Tokyo 162-8666, Japan
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Germaine Cornelissen
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Andi Weydahl
- School of Sport Sciences, The Arctic University of Norway, Campus Alta, N-9509 Alta, Norway
| | - Denis Gubin
- Laboratory for Chronobiology and Chronomedicine, Research Institute of Biomedicine and Biomedical Technologies, Medical University, 625023 Tyumen, Russia
- Department of Biology, Medical University, 625023 Tyumen, Russia
- Tyumen Cardiology Research Center, Tomsk National Research Medical Center, Russian Academy of Science, 634009 Tomsk, Russia
| | - Larry A. Beaty
- Halberg Chronobiology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Masatoshi Murase
- Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502, Japan
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Deppisch P, Kirsch V, Helfrich-Förster C, Senthilan PR. Contribution of cryptochromes and photolyases for insect life under sunlight. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2023; 209:373-389. [PMID: 36609567 PMCID: PMC10102093 DOI: 10.1007/s00359-022-01607-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023]
Abstract
The cryptochrome/photolyase (CRY/PL) family is essential for life under sunlight because photolyases repair UV-damaged DNA and cryptochromes are normally part of the circadian clock that controls the activity-sleep cycle within the 24-h day. In this study, we aim to understand how the lineage and habitat of an insect affects its CRY/PL composition. To this end, we searched the large number of annotated protein sequences of 340 insect species already available in databases for CRY/PLs. Using phylogenetic tree and motif analyses, we identified four frequent CRY/PLs in insects: the photolyases 6-4 PL and CPDII PL, as well as the mammalian-type cryptochrome (MCRY) and Drosophila-type cryptochrome (DCRY). Assignment of CRY/PLs to the corresponding insects confirmed that light-exposed insects tend to have more CRY/PLs than insects with little light exposure. Nevertheless, even insects with greatly reduced CRY/PLs still possess MCRY, which can be regarded as the major insect cryptochrome. Only flies of the genus Schizophora, which includes Drosophila melanogaster, lost MCRY. Moreover, we found that MCRY and CPDII PL as well as DCRY and 6-4 PL occur very frequently together, suggesting an interaction between the two pairs.
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Affiliation(s)
- Peter Deppisch
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Valentina Kirsch
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Charlotte Helfrich-Förster
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany
| | - Pingkalai R Senthilan
- Neurobiology and Genetics, Theodor-Boveri Institute, Biocenter, Julius-Maximilians-University Würzburg, 97074, Würzburg, Germany.
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Calloni G, Vabulas RM. The structural and functional roles of the flavin cofactor FAD in mammalian cryptochromes. Front Mol Biosci 2023; 9:1081661. [PMID: 36660433 PMCID: PMC9845712 DOI: 10.3389/fmolb.2022.1081661] [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: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
The importance of circadian rhythms in human health and disease calls for a thorough understanding of the underlying molecular machinery, including its key components, the flavin adenine dinucleotide (FAD)-containing flavoproteins cryptochrome 1 and 2. Contrary to their Drosophila counterparts, mammalian cryptochromes are direct suppressors of circadian transcription and act independently of light. Light-independence poses the question regarding the role of the cofactor FAD in mammalian cryptochromes. The weak binding of the cofactor in vitro argues against its relevance and might be a functionless evolutionary remnant. From the other side, the FAD-binding pocket constitutes the part of mammalian cryptochromes directly related to their ubiquitylation by the ubiquitin ligase Fbxl3 and is the target for protein-stabilizing small molecules. Increased supplies of FAD stabilize cryptochromes in cell culture, and the depletion of the FAD precursor riboflavin with simultaneous knock-down of riboflavin kinase affects the expression of circadian genes in mice. This review presents the classical and more recent studies in the field, which help to comprehend the role of FAD for the stability and function of mammalian cryptochromes.
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Affiliation(s)
| | - R. Martin Vabulas
- Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany,*Correspondence: R. Martin Vabulas,
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Clyne CD, Kusnadi KP, Cowcher A, Morgan J, Yang J, Fuller PJ, Young MJ. Regulation of mineralocorticoid receptor activation by circadian protein TIMELESS. J Mol Endocrinol 2023; 70:JME-21-0279. [PMID: 36099062 DOI: 10.1530/jme-21-0279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/13/2022] [Indexed: 01/19/2023]
Abstract
The mineralocorticoid receptor (MR) is a ligand-activated transcription factor that regulates cardiorenal physiology and disease. Ligand-dependent MR transactivation involves a conformational change in the MR and recruitment of coregulatory proteins to form a unique DNA-binding complex at the hormone response element in target gene promoters. Differences in the recruitment of coregulatory proteins can promote tissue-, ligand- or gene-specific transcriptional outputs. The goal of this study was to evaluate the circadian protein TIMELESS as a selective regulator of MR transactivation. TIMELESS has an established role in cell cycle regulation and DNA repair. TIMELESS may not be central to mammalian clock function and does not bind DNA; however, RNA and protein levels oscillate over 24 h. Co-expression of TIMELESS down-regulated MR transactivation of an MR-responsive reporter in HEK293 cells, yet enhanced transactivation mediated by other steroid receptors. TIMELESS markedly inhibited MR transactivation of synthetic and native gene promoters and expression of MR target genes in H9c2 cardiac myoblasts. Immunofluorescence showed aldosterone induces colocalisation of TIMELESS and MR, although a direct interaction was not confirmed by coimmunoprecipitation. Potential regulation of circadian clock targets cryptochrome 1 and 2 by TIMELESS was not detected. However, our data suggest that these effects may involve TIMELESS coactivation of oestrogen receptor alpha (ERα). Taken together, these data suggest that TIMELESS may contribute to MR transcriptional outputs via enhancing ERα inhibitory actions on MR transactivation. Given the variable expression of TIMELESS in different cell types, these data offer new opportunities for the development of MR modulators with selective actions.
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Affiliation(s)
- Colin D Clyne
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Kevin P Kusnadi
- Cardiovascular Endocrinology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Alexander Cowcher
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - James Morgan
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Jun Yang
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Peter J Fuller
- Centre for Endocrinology and Metabolism, Hudson Institute of Medical Research, Clayton, Australia
| | - Morag J Young
- Cardiovascular Endocrinology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia
- University of Melbourne and Baker HDI Department of Cardiometabolic Health and Disease, Melbourne, Australia
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Chen SP, Wang DF, Ma WF, Lin XL, Yang G. Knockout of cryptochrome 1 disturbs the locomotor circadian rhythm and development of Plutella xylostella. INSECT SCIENCE 2022. [PMID: 36380712 DOI: 10.1111/1744-7917.13150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/24/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Cryptochrome 1 (CRY1) functions as a light-responsive photoreceptor, which is crucial for circadian rhythms. The identity and function of CRY1 in Plutella xylostella remain unknown. In this study, cry1 was cloned and identified in P. xylostella. Then, a cry1-knockout strain (Cry1-KO) of P. xylostella with a 2-bp deletion was established from the strain Geneva 88 (G88) using the CRISPR/Cas9 technology. No daily temporal oscillation of cry1 was observed in G88 and Cry1-KO, and cry1 mean daily transcription of Cry1-KO was lower than that of G88. Both G88 and Cry1-KO demonstrated rhythmic locomotion under the light/dark condition with Cry1-KO being more active than G88 in the daytime, whereas Cry1-KO completely lost rhythmicity under constant darkness. The developmental period of pre-adult of Cry1-KO was longer than that of G88; the lifespan of the Cry1-KO male adult was shorter than that of G88; the fecundity of Cry1-KO was lower than that of G88; and Cry1-KO showed lower intrinsic rate of increase (r), net reproduction rate (R0 ), finite increase rate (λ), and longer mean generation time (T) than G88. Our results indicate that cry1 is involved in the regulation of locomotor circadian rhythm and development in P. xylostella, providing a potential target gene for controlling the pest and a basis for further investigation on circadian rhythms in lepidopterans.
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Affiliation(s)
- Shao-Ping Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Dan-Feng Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Wei-Feng Ma
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Xiao-Lu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Center for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, Fuzhou, China
- Key Laboratory of Green Pest Control (Fujian Agriculture and Forestry University), Fujian Province University, Fuzhou, China
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Level of constitutively expressed BMAL1 affects the robustness of circadian oscillations. Sci Rep 2022; 12:19519. [PMID: 36376366 PMCID: PMC9663716 DOI: 10.1038/s41598-022-24188-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/11/2022] [Indexed: 11/15/2022] Open
Abstract
The circadian rhythm is a biological oscillation of physiological activities with a period of approximately 24 h, that is driven by a cell-autonomous oscillator called the circadian clock. The current model of the mammalian circadian clock is based on a transcriptional-translational negative feedback loop in which the protein products of clock genes accumulate in a circadian manner and repress their own transcription. However, several studies have revealed that constitutively expressed clock genes can maintain circadian oscillations. To understand the underlying mechanism, we expressed Bmal1 in Bmal1-disrupted cells using a doxycycline-inducible promoter and monitored Bmal1 and Per2 promoter activity using luciferase reporters. Although the levels of BMAL1 and other clock proteins, REV-ERBα and CLOCK, showed no obvious rhythmicity, robust circadian oscillation in Bmal1 and Per2 promoter activities with the correct phase relationship was observed, which proceeded in a doxycycline-concentration-dependent manner. We applied transient response analysis to the Bmal1 promoter activity in the presence of various doxycycline concentrations. Based on the obtained transfer functions, we suggest that, at least in our experimental system, BMAL1 is not directly involved in the oscillatory process, but modulates the oscillation robustness by regulating basal clock gene promoter activity.
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Yagi M, Miller S, Nagai Y, Inuki S, Sato A, Hirota T. A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins. F1000Res 2022; 11:1016. [PMID: 36226040 PMCID: PMC9523283 DOI: 10.12688/f1000research.124658.2] [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] [Accepted: 10/26/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Impairment of the circadian clock has been associated with numerous diseases, including sleep disorders and metabolic disease. Although small molecules that modulate clock function may form the basis of drug discovery of clock-related diseases, only a few compounds that selectively target core clock proteins have been identified. Three scaffolds were previously discovered as small-molecule activators of the clock protein Cryptochrome (CRY), and they have been providing powerful tools to understand and control the circadian clock system. Identifying new scaffolds will expand the possibilities of drug discovery. Methods: A methylbenzimidazole derivative TH401 identified from cell-based circadian screens was characterized. Effects of TH401 on circadian rhythms were evaluated in cellular assays. Functional assays and X-ray crystallography were used to elucidate the effects of the compound on CRY1 and CRY2 isoforms. Results: TH401 lengthened the period of circadian rhythms and stabilized both CRY1 and CRY2. The compound repressed Per2 reporter activity, which was reduced by Cry1 or Cry2 knockout and abolished by Cry1/Cry2 double knockout, indicating the dependence on CRY isoforms. Thermal shift assays showed slightly higher interaction of TH401 with CRY2 over CRY1. The crystal structure of CRY1 in complex with TH401 revealed a conformational change of the gatekeeper W399, which is involved in isoform-selectivity determination. Conclusions: The present study identified a new small molecule TH401 that targets both CRY isoforms. This compound has expanded the chemical diversity of CRY activators, and will ultimately aid in the development of therapeutics against circadian clock-related disorders.
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Affiliation(s)
- Moeri Yagi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan,
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Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes. Int J Mol Sci 2022; 23:ijms231911135. [PMID: 36232445 PMCID: PMC9570262 DOI: 10.3390/ijms231911135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.
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Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O. Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. SCIENCE ADVANCES 2022; 8:eabo6467. [PMID: 36112690 PMCID: PMC9481131 DOI: 10.1126/sciadv.abo6467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/02/2022] [Indexed: 05/25/2023]
Abstract
Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.
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Affiliation(s)
- Mieka Rinsky
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Eviatar Weizman
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Hiba Waldman Ben-Asher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Gal Eyal
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
- ARC Centre of Excellence for Coral Reef Studies, School of Biological Sciences, University of Queensland St. Lucia, Queensland 4072, Australia
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
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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: 24] [Impact Index Per Article: 8.0] [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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Smies CW, Bodinayake KK, Kwapis JL. Time to learn: The role of the molecular circadian clock in learning and memory. Neurobiol Learn Mem 2022; 193:107651. [PMID: 35697314 PMCID: PMC9903177 DOI: 10.1016/j.nlm.2022.107651] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 12/27/2022]
Abstract
The circadian system plays an important role in aligning biological processes with the external time of day. A range of physiological functions are governed by the circadian cycle, including memory processes, yet little is understood about how the clock interfaces with memory at a molecular level. The molecular circadian clock consists of four key genes/gene families, Period, Clock, Cryptochrome, and Bmal1, that rhythmically cycle in an ongoing transcription-translation negative feedback loop that maintains an approximately 24-hour cycle within cells of the brain and body. In addition to their roles in generating the circadian rhythm within the brain's master pacemaker (the suprachiasmatic nucleus), recent research has suggested that these clock genes may function locally within memory-relevant brain regions to modulate memory across the day/night cycle. This review will discuss how these clock genes function both within the brain's central clock and within memory-relevant brain regions to exert circadian control over memory processes. For each core clock gene, we describe the current research that demonstrates a potential role in memory and outline how these clock genes might interface with cascades known to support long-term memory formation. Together, the research suggests that clock genes function locally within satellite clocks across the brain to exert circadian control over long-term memory formation and possibly other biological processes. Understanding how clock genes might interface with local molecular cascades in the hippocampus and other brain regions is a critical step toward developing treatments for the myriad disorders marked by dysfunction of both the circadian system and cognitive processes.
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Affiliation(s)
- Chad W Smies
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kasuni K Bodinayake
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Janine L Kwapis
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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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: 2] [Impact Index Per Article: 0.7] [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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Alachkar A. Aromatic patterns: Tryptophan aromaticity as a catalyst for the emergence of life and rise of consciousness. Phys Life Rev 2022; 42:93-114. [PMID: 35905538 DOI: 10.1016/j.plrev.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022]
Abstract
Sunlight held the key to the origin of life on Earth. The earliest life forms, cyanobacteria, captured the sunlight to generate energy through photosynthesis. Life on Earth evolved in accordance with the circadian rhythms tied to sensitivity to sunlight patterns. A unique feature of cyanobacterial photosynthetic proteins and circadian rhythms' molecules, and later of nearly all photon-sensing molecules throughout evolution, is that the aromatic amino acid tryptophan (Trp) resides at the center of light-harvesting active sites. In this perspective, I review the literature and integrate evidence from different scientific fields to explore the role Trp plays in photon-sensing capabilities of living organisms through its resonance delocalization of π-electrons. The observations presented here are the product of apparently unrelated phenomena throughout evolution, but nevertheless share consistent patterns of photon-sensing by Trp-containing and Trp-derived molecules. I posit the unique capacity to transfer electrons during photosynthesis in the earliest life forms is conferred to Trp due to its aromaticity. I propose this ability evolved to assume more complex functions, serving as a host for mechanisms underlying mental aptitudes - a concept which provides a theoretical basis for defining the neural correlates of consciousness. The argument made here is that Trp aromaticity may have allowed for the inception of the mechanistic building blocks used to fabricate complexity in higher forms of life. More specifically, Trp aromatic non-locality may have acted as a catalyst for the emergence of consciousness by instigating long-range synchronization and stabilizing the large-scale coherence of neural networks, which mediate functional brain activity. The concepts proposed in this perspective provide a conceptual foundation that invites further interdisciplinary dialogue aimed at examining and defining the role of aromaticity (beyond Trp) in the emergence of life and consciousness.
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Affiliation(s)
- Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA; UC Irvine Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA.
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44
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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: 18] [Impact Index Per Article: 6.0] [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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45
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Kim YY, Jang H, Lee G, Jeon YG, Sohn JH, Han JS, Lee WT, Park J, Huh JY, Nahmgoong H, Han SM, Kim J, Pak M, Kim S, Kim JS, Kim JB. Hepatic GSK3β-Dependent CRY1 Degradation Contributes to Diabetic Hyperglycemia. Diabetes 2022; 71:1373-1387. [PMID: 35476750 DOI: 10.2337/db21-0649] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/06/2022] [Indexed: 11/13/2022]
Abstract
Excessive hepatic glucose production (HGP) is a key factor promoting hyperglycemia in diabetes. Hepatic cryptochrome 1 (CRY1) plays an important role in maintaining glucose homeostasis by suppressing forkhead box O1 (FOXO1)-mediated HGP. Although downregulation of hepatic CRY1 appears to be associated with increased HGP, the mechanism(s) by which hepatic CRY1 dysregulation confers hyperglycemia in subjects with diabetes is largely unknown. In this study, we demonstrate that a reduction in hepatic CRY1 protein is stimulated by elevated E3 ligase F-box and leucine-rich repeat protein 3 (FBXL3)-dependent proteasomal degradation in diabetic mice. In addition, we found that GSK3β-induced CRY1 phosphorylation potentiates FBXL3-dependent CRY1 degradation in the liver. Accordingly, in diabetic mice, GSK3β inhibitors effectively decreased HGP by facilitating the effect of CRY1-mediated FOXO1 degradation on glucose metabolism. Collectively, these data suggest that tight regulation of hepatic CRY1 protein stability is crucial for maintaining systemic glucose homeostasis.
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Affiliation(s)
- Ye Young Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Hagoon Jang
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Gung Lee
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Yong Geun Jeon
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jee Hyung Sohn
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Ji Seul Han
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Won Taek Lee
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jeu Park
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jin Young Huh
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Hahn Nahmgoong
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Sang Mun Han
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, School of Biological Sciences, Seoul, South Korea
| | - Minwoo Pak
- Department of Computer Science and Engineering, Institute of Engineering Research, Seoul National University, Seoul, South Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Institute of Engineering Research, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, South Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, School of Biological Sciences, Seoul, South Korea
| | - Jae Bum Kim
- Center for Adipocyte Structure and Function, Institute of Molecular Biology and Genetics, School of Biological Sciences, Seoul National University, Seoul, South Korea
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46
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Hoyt KR, Obrietan K. Circadian clocks, cognition, and Alzheimer's disease: synaptic mechanisms, signaling effectors, and chronotherapeutics. Mol Neurodegener 2022; 17:35. [PMID: 35525980 PMCID: PMC9078023 DOI: 10.1186/s13024-022-00537-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 04/08/2022] [Indexed: 12/20/2022] Open
Abstract
Modulation of basic biochemical and physiological processes by the circadian timing system is now recognized as a fundamental feature of all mammalian organ systems. Within the central nervous system, these clock-modulating effects are reflected in some of the most complex behavioral states including learning, memory, and mood. How the clock shapes these behavioral processes is only now beginning to be realized. In this review we describe recent findings regarding the complex set of cellular signaling events, including kinase pathways, gene networks, and synaptic circuits that are under the influence of the clock timing system and how this, in turn, shapes cognitive capacity over the circadian cycle. Further, we discuss the functional roles of the master circadian clock located in the suprachiasmatic nucleus, and peripheral oscillator populations within cortical and limbic circuits, in the gating of synaptic plasticity and memory over the circadian cycle. These findings are then used as the basis to discuss the connection between clock dysregulation and cognitive impairments resulting from Alzheimer's disease (AD). In addition, we discuss the conceptually novel idea that in AD, there is a selective disruption of circadian timing within cortical and limbic circuits, and that it is the disruption/desynchronization of these regions from the phase-entraining effects of the SCN that underlies aspects of the early- and mid-stage cognitive deficits in AD. Further, we discuss the prospect that the disruption of circadian timing in AD could produce a self-reinforcing feedback loop, where disruption of timing accelerates AD pathogenesis (e.g., amyloid deposition, oxidative stress and cell death) that in turn leads to a further disruption of the circadian timing system. Lastly, we address potential therapeutic approaches that could be used to strengthen cellular timing networks and, in turn, how these approaches could be used to improve cognitive capacity in Alzheimer's patients.
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Affiliation(s)
- Kari R Hoyt
- Division of Pharmaceutics and Pharmacology, Ohio State University, 412 Riffe Building, 12th Ave, Columbus, OH, 43210, USA.
| | - Karl Obrietan
- Department of Neuroscience, Ohio State University, Graves Hall, 333 W. 10th Ave, Columbus, OH, 43210, USA.
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47
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Hirase S, Kumai Y, Kato S, Hagihara S, Kikuchi K, Kuroki M. Genomic signatures for latitudinal selection in the tropical eel Anguilla marmorata. J Evol Biol 2022; 35:763-771. [PMID: 35324039 DOI: 10.1111/jeb.13995] [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: 08/26/2021] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
Selection acting across environmental gradients, such as latitudes, can cause spatial structuring of genomic variants even within panmictic populations. In this study, we focused on the within-generation latitudinal selection between northernmost and southernmost individuals of the North Pacific population of a tropical eel Anguilla marmorata, which shares its northernmost distribution with a temperate eel Anguilla japonica. Whole-genome sequencing data indicated that the northernmost and southernmost individuals of A. marmorata belong to a single panmictic population, as suggested by previous studies. On the contrary, parts of genomic regions across multiple chromosomes exhibited significant genetic differentiation between the northernmost and southernmost individuals, and in these genomic regions, the genotypes of the northernmost individuals were similar to those of A. japonica. These findings suggested within-generation latitudinal selection of A. marmorata, which might have led to genetic closeness between northernmost A. marmorata and A. japonica.
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Affiliation(s)
- Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Japan
| | - Yusuke Kumai
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Shuya Kato
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Japan
| | - Seishi Hagihara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Japan
| | - Mari Kuroki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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48
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Tseng E, Underwood JG, Evans Hutzenbiler BD, Trojahn S, Kingham B, Shevchenko O, Bernberg E, Vierra M, Robbins CT, Jansen HT, Kelley JL. Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos). G3 (BETHESDA, MD.) 2022; 12:6472356. [PMID: 35100340 PMCID: PMC9210309 DOI: 10.1093/g3journal/jkab422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022]
Abstract
Understanding hibernation in brown bears (Ursus arctos) can provide insight into some human diseases. During hibernation, brown bears experience periods of insulin resistance, physical inactivity, extreme bradycardia, obesity, and the absence of urine production. These states closely mimic aspects of human diseases such as type 2 diabetes, muscle atrophy, as well as renal and heart failure. The reversibility of these states from hibernation to active season enables the identification of mediators with possible therapeutic value for humans. Recent studies have identified genes and pathways that are differentially expressed between active and hibernation seasons in bears. However, little is known about the role of differential expression of gene isoforms on hibernation physiology. To identify both distinct and novel mRNA isoforms, full-length RNA-sequencing (Iso-Seq) was performed on adipose, skeletal muscle, and liver from three individual bears sampled during both active and hibernation seasons. The existing reference genome annotation was improved by combining it with the Iso-Seq data. Short-read RNA-sequencing data from six individuals were mapped to the new reference annotation to quantify differential isoform usage (DIU) between tissues and seasons. We identified differentially expressed isoforms in all three tissues, to varying degrees. Adipose had a high level of DIU with isoform switching, regardless of whether the genes were differentially expressed. Our analyses revealed that DIU, even in the absence of differential gene expression, is an important mechanism for modulating genes during hibernation. These findings demonstrate the value of isoform expression studies and will serve as the basis for deeper exploration into hibernation biology.
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Affiliation(s)
| | | | - Brandon D Evans Hutzenbiler
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA.,School of the Environment, Washington State University, Pullman, WA 99164, USA
| | - Shawn Trojahn
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Brewster Kingham
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Olga Shevchenko
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | - Erin Bernberg
- Sequencing & Genotyping Center, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
| | | | - Charles T Robbins
- School of the Environment, Washington State University, Pullman, WA 99164, USA.,School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Heiko T Jansen
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA 99164, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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49
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Zhang C, Ni P, Liang S, Li X, Tian Y, Du X, Wei W, Meng Y, Wei J, Ma X, Deng W, Guo W, Li M, Yu H, Zhao L, Wang Q, Pak SC, Li T. Alterations in CRY2 and PER3 gene expression associated with thalamic-limbic community structural abnormalities in patients with bipolar depression or unipolar depression. J Affect Disord 2022; 298:472-480. [PMID: 34732337 DOI: 10.1016/j.jad.2021.10.125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/30/2021] [Accepted: 10/20/2021] [Indexed: 02/05/2023]
Abstract
Objectives The current study aimed to identify shared and distinct brain structure abnormalities and their relationships with the expression of circadian genes in patients with bipolar or unipolar depression. Method A total of 93 subjects participated in this study, including 32 patients with bipolar depression (BDP), 26 patients with unipolar depression (UDP) and 35 age- and sex-matched healthy controls. Brain structural magnetic resonance imaging scans were obtained, and optimized voxel-based morphometry was used to explore group differences in regional gray matter volume (GMV). The mRNA expression levels of circadian genes in peripheral blood were measured using reverse transcription quantitative real-time polymerase chain reaction. Results Our results showed that the GMV in brain regions in the thalamus-limbic pathways had significantly increased in the BDP patients compared to controls, while the increased GMV in UDP patients compared to controls was limited to the thalamus. The mRNA expression levels of circadian-related genes decreased significantly in patients with BDP, but increased in patients with UDP, compared to controls. In addition, the GMV in the right thalamus in the patients with UDP was positively associated with mRNA levels of CRY2, while the GMV in the right hippocampus in the patients with BDP was negatively associated with mRNA levels of PER3. Conclusion Our study suggested that patients with BDP or MDD shared GMV abnormalities in the right thalamus. The PER3 and CRY2 genes might be critical to right hippocampal dysfunction in BDP and right thalamic dysfunction in UDP, respectively. The result provided potentially important molecular targets for the treatment of mood disorders.
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Affiliation(s)
- Chengcheng Zhang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Peiyan Ni
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Sugai Liang
- Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaojing Li
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yang Tian
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xiangdong Du
- Suzhou Psychiatric Hospital, The Affiliated Guangji Hospital of Soochow University, China
| | - Wei Wei
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Yajing Meng
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Jinxue Wei
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Xiaohong Ma
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wei Deng
- Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Wanjun Guo
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Mingli Li
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Hua Yu
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Liansheng Zhao
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Qiang Wang
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Sham C Pak
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China; Centre for PanorOmic Sciences, The University of Hong Kong, Hong Kong, SAR, China; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Tao Li
- Mental Health Center and Psychiatric Laboratory, the State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, Sichuan, China; Affiliated Mental Health Center and Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China.
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50
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Role of Sleep Restriction in Daily Rhythms of Expression of Hypothalamic Core Clock Genes in Mice. Curr Issues Mol Biol 2022; 44:609-625. [PMID: 35723328 PMCID: PMC8929085 DOI: 10.3390/cimb44020042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
Lack of sleep time is a menace to modern people, and it leads to chronic diseases and mental illnesses. Circadian processes control sleep, but little is known about how sleep affects the circadian system. Therefore, we performed a 28-day sleep restriction (SR) treatment in mice. Sleep restriction disrupted the clock genes’ circadian rhythm. The circadian rhythms of the Cry1 and Per1/2/3 genes disappeared. The acrophase of the clock genes (Bmal1, Clock, Rev-erbα, and Rorβ) that still had a circadian rhythm was advanced, while the acrophase of negative clock gene Cry2 was delayed. Clock genes’ upstream signals ERK and EIFs also had circadian rhythm disorders. Accompanied by changes in the central oscillator, the plasma output signal (melatonin, corticosterone, IL-6, and TNF-α) had an advanced acrophase. While the melatonin mesor was decreased, the corticosterone, IL-6, and TNF-α mesor was increased. Our results indicated that chronic sleep loss could disrupt the circadian rhythm of the central clock through ERK and EIFs and affect the output signal downstream of the core biological clock.
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