1
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Dhungana P, Wei X, Meuti ME, Sim C. Genome-wide identification of PAR domain protein 1 (PDP1) targets through ChIP-seq reveals the regulation of diapause-specific characteristics in Culex pipiens. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38989821 DOI: 10.1111/imb.12943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
Insects use seasonal diapause as an alternative strategy to endure adverse seasons. This developmental trajectory is induced by environmental cues like short-day lengths in late summer and early fall, but how insects measure day length is unknown. The circadian clock has been implicated in regulating photoperiodic or seasonal responses in many insects, including the Northern house mosquito, Culex pipiens, which enters adult diapause. To investigate the potential control of diapause by circadian control, we employed ChIP-sequencing to identify the downstream targets of a circadian transcription factor, PAR domain protein 1 (PDP1), that contribute to the hallmark features of diapause. We identified the nearest genes in a 10 kb region of the anticipated PDP1 binding sites, listed prospective targets and searched for PDP1-specific binding sites. By examining the functional relevance to diapause-specific behaviours and modifications such as metabolic pathways, lifespan extension, cell cycle regulation and stress tolerance, eight genes were selected as targets and validated using ChIP-qPCR. In addition, qRT-PCR demonstrated that the mRNA abundance of PDP1 targets increased in the heads of diapausing females during the middle of the scotophase (ZT17) compared with the early photophase (ZT1), in agreement with the peak and trough of PDP1 abundance. Thus, our investigation uncovered the mechanism by which PDP1 might generate a diapause phenotype in insects.
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Affiliation(s)
| | - Xueyan Wei
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Megan E Meuti
- Department of Entomology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, Ohio, USA
| | - Cheolho Sim
- Department of Biology, Baylor University, Waco, Texas, USA
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2
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Fu H, Fei C, Ouyang Q, Tu Y. Temperature compensation through kinetic regulation in biochemical oscillators. Proc Natl Acad Sci U S A 2024; 121:e2401567121. [PMID: 38748573 PMCID: PMC11127053 DOI: 10.1073/pnas.2401567121] [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: 01/23/2024] [Accepted: 04/15/2024] [Indexed: 05/27/2024] Open
Abstract
Nearly all circadian clocks maintain a period that is insensitive to temperature changes, a phenomenon known as temperature compensation (TC). Yet, it is unclear whether there is any common feature among different systems that exhibit TC. From a general timescale invariance, we show that TC relies on the existence of certain period-lengthening reactions wherein the period of the system increases strongly with the rates in these reactions. By studying several generic oscillator models, we show that this counterintuitive dependence is nonetheless a common feature of oscillators in the nonlinear (far-from-onset) regime where the oscillation can be separated into fast and slow phases. The increase of the period with the period-lengthening reaction rates occurs when the amplitude of the slow phase in the oscillation increases with these rates while the progression speed in the slow phase is controlled by other rates of the system. The positive dependence of the period on the period-lengthening rates balances its inverse dependence on other kinetic rates in the system, which gives rise to robust TC in a wide range of parameters. We demonstrate the existence of such period-lengthening reactions and their relevance for TC in all four model systems we considered. Theoretical results for a model of the Kai system are supported by experimental data. A study of the energy dissipation also shows that better TC performance requires higher energy consumption. Our study unveils a general mechanism by which a biochemical oscillator achieves TC by operating in parameter regimes far from the onset where period-lengthening reactions exist.
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Affiliation(s)
- Haochen Fu
- Department of Physics, University of California, San Diego, La Jolla, CA 92093
| | - Chenyi Fei
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, People's Republic of China
| | - Yuhai Tu
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598
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3
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Hoekstra MMB, Ness N, Badia-Soteras A, Brancaccio M. Bmal1 integrates circadian function and temperature sensing in the suprachiasmatic nucleus. Proc Natl Acad Sci U S A 2024; 121:e2316646121. [PMID: 38625943 PMCID: PMC11047078 DOI: 10.1073/pnas.2316646121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/22/2024] [Indexed: 04/18/2024] Open
Abstract
Circadian regulation and temperature dependency are important orchestrators of molecular pathways. How the integration between these two drivers is achieved, is not understood. We monitored circadian- and temperature-dependent effects on transcription dynamics of cold-response protein RNA Binding Motif 3 (Rbm3). Temperature changes in the mammalian master circadian pacemaker, the suprachiasmatic nucleus (SCN), induced Rbm3 transcription and regulated its circadian periodicity, whereas the core clock gene Per2 was unaffected. Rbm3 induction depended on a full Brain And Muscle ARNT-Like Protein 1 (Bmal1) complement: reduced Bmal1 erased Rbm3 responses and weakened SCN circuit resilience to temperature changes. By focusing on circadian and temperature dependency, we highlight weakened transmission between core clock and downstream pathways as a potential route for reduced circadian resilience.
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Affiliation(s)
- Marieke M. B. Hoekstra
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Natalie Ness
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Aina Badia-Soteras
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
| | - Marco Brancaccio
- Department of Brain Science, Imperial College London, LondonW12 0NN, United Kingdom
- Department of Brain Sciences, United Kingdom Dementia Research Institute at Imperial College London, LondonW12 0NN, United Kingdom
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4
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Hiroki S, Yoshitane H. Ror homolog nhr-23 is essential for both developmental clock and circadian clock in C. elegans. Commun Biol 2024; 7:243. [PMID: 38418700 PMCID: PMC10902330 DOI: 10.1038/s42003-024-05894-3] [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: 06/05/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Animals have internal clocks that generate biological rhythms. In mammals, clock genes such as Period form the circadian clock to generate approximately 24-h biological rhythms. In C. elegans, the clock gene homologs constitute the "developmental clock", which has an 8-h period during larval development to determine the timing of molting. Thus, the ancestral circadian clock has been believed to evolve into the oscillator with a shorter period in C. elegans. However, circadian rhythms have also been observed in adult C. elegans, albeit relatively weak. This prompts the question: if the clock gene homologs drive the developmental rhythm with 8-h period, which genes generate the circadian rhythms in C. elegans? In this study, we discovered that nhr-23, a homolog of the mammalian circadian clock gene Ror, is essential for circadian transcriptional rhythms in adult C. elegans. Interestingly, nhr-23 was also known to be essential for the molting clock. The bilaterian ancestral circadian clock genes might have evolved to function over multiple periods depending on developmental contexts rather than a single 8-h period in C. elegans.
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Affiliation(s)
- Shingo Hiroki
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
| | - Hikari Yoshitane
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan.
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5
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Hiro S, Kobayashi K, Nemoto T, Enoki R. In-phasic cytosolic-nuclear Ca 2+ rhythms in suprachiasmatic nucleus neurons. Front Neurosci 2023; 17:1323565. [PMID: 38178840 PMCID: PMC10765503 DOI: 10.3389/fnins.2023.1323565] [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: 10/18/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
The suprachiasmatic nucleus (SCN) of the hypothalamus is the master circadian clock in mammals. SCN neurons exhibit circadian Ca2+ rhythms in the cytosol, which is thought to act as a messenger linking the transcriptional/translational feedback loop (TTFL) and physiological activities. Transcriptional regulation occurs in the nucleus in the TTFL model, and Ca2+-dependent kinase regulates the clock gene transcription. However, the Ca2+ regulatory mechanisms between cytosol and nucleus as well as the ionic origin of Ca2+ rhythms remain unclear. In the present study, we monitored circadian-timescale Ca2+ dynamics in the nucleus and cytosol of SCN neurons at the single-cell and network levels. We observed robust nuclear Ca2+ rhythm in the same phase as the cytosolic rhythm in single SCN neurons and entire regions. Neuronal firing inhibition reduced the amplitude of both nuclear and cytosolic Ca2+ rhythms, whereas blocking of Ca2+ release from the endoplasmic reticulum (ER) via ryanodine and inositol 1,4,5-trisphosphate (IP3) receptors had a minor effect on either Ca2+ rhythms. We conclude that the in-phasic circadian Ca2+ rhythms in the cytosol and nucleus are mainly driven by Ca2+ influx from the extracellular space, likely through the nuclear pore. It also raises the possibility that nuclear Ca2+ rhythms directly regulate transcription in situ.
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Affiliation(s)
- Sota Hiro
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
| | - Kenta Kobayashi
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- Section of Viral Vector Development, National Institute for Physiological Sciences, Okazaki, Aichi, Japan
| | - Tomomi Nemoto
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
| | - Ryosuke Enoki
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
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6
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Choquet M, Lenner F, Cocco A, Toullec G, Corre E, Toullec JY, Wallberg A. Comparative Population Transcriptomics Provide New Insight into the Evolutionary History and Adaptive Potential of World Ocean Krill. Mol Biol Evol 2023; 40:msad225. [PMID: 37816123 PMCID: PMC10642690 DOI: 10.1093/molbev/msad225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/31/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Genetic variation is instrumental for adaptation to changing environments but it is unclear how it is structured and contributes to adaptation in pelagic species lacking clear barriers to gene flow. Here, we applied comparative genomics to extensive transcriptome datasets from 20 krill species collected across the Atlantic, Indian, Pacific, and Southern Oceans. We compared genetic variation both within and between species to elucidate their evolutionary history and genomic bases of adaptation. We resolved phylogenetic interrelationships and uncovered genomic evidence to elevate the cryptic Euphausia similis var. armata into species. Levels of genetic variation and rates of adaptive protein evolution vary widely. Species endemic to the cold Southern Ocean, such as the Antarctic krill Euphausia superba, showed less genetic variation and lower evolutionary rates than other species. This could suggest a low adaptive potential to rapid climate change. We uncovered hundreds of candidate genes with signatures of adaptive evolution among Antarctic Euphausia but did not observe strong evidence of adaptive convergence with the predominantly Arctic Thysanoessa. We instead identified candidates for cold-adaptation that have also been detected in Antarctic fish, including genes that govern thermal reception such as TrpA1. Our results suggest parallel genetic responses to similar selection pressures across Antarctic taxa and provide new insights into the adaptive potential of important zooplankton already affected by climate change.
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Affiliation(s)
- Marvin Choquet
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Felix Lenner
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Arianna Cocco
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Gaëlle Toullec
- Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Erwan Corre
- CNRS, Sorbonne Université, FR 2424, ABiMS Platform, Station Biologique de Roscoff, Roscoff, France
| | - Jean-Yves Toullec
- CNRS, UMR 7144, AD2M, Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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7
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Schmal C, Maier B, Ashwal-Fluss R, Bartok O, Finger AM, Bange T, Koutsouli S, Robles MS, Kadener S, Herzel H, Kramer A. Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock. PLoS Biol 2023; 21:e3002164. [PMID: 37379316 DOI: 10.1371/journal.pbio.3002164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
A defining property of circadian clocks is temperature compensation, characterized by the resilience of their near 24-hour free-running periods against changes in environmental temperature within the physiological range. While temperature compensation is evolutionary conserved across different taxa of life and has been studied within many model organisms, its molecular underpinnings remain elusive. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions. Here, we show that knockdown of cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a key regulator of 3'-end cleavage and polyadenylation, significantly alters circadian temperature compensation in human U-2 OS cells. We apply a combination of 3'-end-RNA-seq and mass spectrometry-based proteomics to globally quantify changes in 3' UTR length as well as gene and protein expression between wild-type and CPSF6 knockdown cells and their dependency on temperature. Since changes in temperature compensation behavior should be reflected in alterations of temperature responses within one or all of the 3 regulatory layers, we statistically assess differential responses upon changes in ambient temperature between wild-type and CPSF6 knockdown cells. By this means, we reveal candidate genes underlying circadian temperature compensation, including eukaryotic translation initiation factor 2 subunit 1 (EIF2S1).
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bert Maier
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Reut Ashwal-Fluss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anna-Marie Finger
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Stella Koutsouli
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Maria S Robles
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Kadener
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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8
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Baruah D, Marak CNK, Roy A, Gohain D, Kumar A, Das P, Borkovich KA, Tamuli R. Multiple calcium signaling genes play a role in the circadian period of Neurospora crassa. FEMS Microbiol Lett 2023; 370:fnad044. [PMID: 37193664 PMCID: PMC10237334 DOI: 10.1093/femsle/fnad044] [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: 06/15/2022] [Revised: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 05/18/2023] Open
Abstract
The Ca2+ signaling genes cpe-1, plc-1, ncs-1, splA2, camk-1, camk-2, camk-3, camk-4, cmd, and cnb-1 are necessary for a normal circadian period length in Neurospora crassa. In addition, the Q10 values ranged between 0.8 and 1.2 for the single mutants lacking cpe-1, splA2, camk-1, camk-2, camk-3, camk-4, and cnb-1, suggesting that the circadian clock exhibits standard temperature compensation. However, the Q10 value for the ∆plc-1 mutant was 1.41 at 25 and 30 °C, 1.53 and 1.40 for the ∆ncs-1 mutant at 20 and 25 °C, and at 20 and 30 °C, respectively, suggesting a partial loss of temperature compensation in these two mutants. Moreover, expression of frq, a regulator of the circadian period, and the blue light receptor wc-1, were increased >2-fold in the Δplc-1, ∆plc-1; ∆cpe-1, and the ∆plc-1; ∆splA2 mutants at 20 °C. The frq mRNA level was increased >2-fold in the Δncs-1 mutant compared to the ras-1bd strain at 20 °C. Therefore, multiple Ca2+ signaling genes regulate the circadian period, by influencing expression of the frq and wc-1 genes that are critical for maintaining the normal circadian period length in N. crassa.
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Affiliation(s)
- Darshana Baruah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Christy Noche K Marak
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Avishek Roy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Dibakar Gohain
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ajeet Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Pallavi Das
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Katherine A Borkovich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, College of Natural and Agricultural Sciences, University of California Riverside, Riverside 92521, CA, USA
| | - Ranjan Tamuli
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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9
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Ono D, Wang H, Hung CJ, Wang HT, Kon N, Yamanaka A, Li Y, Sugiyama T. Network-driven intracellular cAMP coordinates circadian rhythm in the suprachiasmatic nucleus. SCIENCE ADVANCES 2023; 9:eabq7032. [PMID: 36598978 PMCID: PMC11318661 DOI: 10.1126/sciadv.abq7032] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The mammalian central circadian clock, located in the suprachiasmatic nucleus (SCN), coordinates the timing of physiology and behavior to local time cues. In the SCN, second messengers, such as cAMP and Ca2+, are suggested to be involved in the input and/or output of the molecular circadian clock. However, the functional roles of second messengers and their dynamics in the SCN remain largely unclear. In the present study, we visualized the spatiotemporal patterns of circadian rhythms of second messengers and neurotransmitter release in the SCN. Here, we show that neuronal activity regulates the rhythmic release of vasoactive intestinal peptides from the SCN, which drives the circadian rhythms of intracellular cAMP in the SCN. Furthermore, optical manipulation of intracellular cAMP levels in the SCN shifts molecular and behavioral circadian rhythms. Together, our study demonstrates that intracellular cAMP is a key molecule in the organization of the SCN circadian neuronal network.
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Affiliation(s)
- Daisuke Ono
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
| | - Chi Jung Hung
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Neural Regulation, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hsin-tzu Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Biological Sciences, School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Naohiro Kon
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Akihiro Yamanaka
- Chinese Institute for Brain Research (CIBR), Beijing, 102206, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
| | - Takashi Sugiyama
- Advanced Optics and Biological Engineering, Evident Corporation, Tokyo, Japan
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10
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Yamada Y, Ito H, Maeda S. Artificial temperature-compensated biological clock using temperature-sensitive Belousov-Zhabotinsky gels. Sci Rep 2022; 12:22436. [PMID: 36575287 PMCID: PMC9794784 DOI: 10.1038/s41598-022-27014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
The circadian rhythm is a fundamental physiological function for a wide range of organisms. The molecular machinery for generating rhythms has been elucidated over the last few decades. Nevertheless, the mechanism for temperature compensation of the oscillation period, which is a prominent property of the circadian rhythm, is still controversial. In this study, we propose a new mechanism through a chemically synthetic approach (i.e., we realized temperature compensation by the Belousov-Zhabotinsky (BZ) gels). The BZ gels are prepared by embedding a metal catalyst of the BZ reaction into the gel polymer. We made the body of BZ gels using a temperature-sensitive polymer gel, which enabled temperature compensation of the oscillation by using temperature dependence of volume. Moreover, we constructed a simple mathematical model for the BZ oscillation in temperature-sensitive gels. The model can reproduce temperature compensation of BZ gels, even though all reactions are temperature sensitive according to the Arrhenius rule. Our finding hints that a soft body coupling may be underlying temperature-compensated biological functions, including circadian rhythms.
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Affiliation(s)
- Yuhei Yamada
- Living Systems Materialogy Research Group, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259, Nagatsuta-Cho, Midori-Ku, Yokohama, 226-8501, Japan.
| | - Hiroshi Ito
- Faculty of Design, Kyushu University, 4-9-1 Shiobaru Minami-Ku, Fukuoka, 815-8540, Japan
| | - Shingo Maeda
- Living Systems Materialogy Research Group, International Research Frontiers Initiative, Tokyo Institute of Technology, 4259, Nagatsuta-Cho, Midori-Ku, Yokohama, 226-8501, Japan
- Department of Mechanical Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama Meguro-Ku, Tokyo, 152-8550, Japan
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11
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Wang HT, Miyairi S, Kitamura M, Iizuka K, Asano Y, Yoshimura T, Kon N. Real time monitoring of cold Ca 2+ dependent transcription and its modulation by NCX inhibitors. Sci Rep 2022; 12:17325. [PMID: 36243739 PMCID: PMC9569354 DOI: 10.1038/s41598-022-22166-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/11/2022] [Indexed: 01/10/2023] Open
Abstract
Real-time monitoring of cellular temperature responses is an important technique in thermal biology and drug development. Recent study identified that Na+/Ca2+ exchanger (NCX)-dependent Ca2+ influx transduces cold signals to circadian clock in mammalian cultured cells. The finding raised an idea that cellular responses to the cold signals can be analyzed by monitoring of clock gene expression. We found that Per1 and Per2 were up-regulated after culture at 27 °C compared to 37 °C in Rat-1 fibroblasts. In order to monitor cold-Ca2+-dependent transcription in living cells, we developed a luciferase-based real-time reporting system by using Per1 promoter, Per2 promoter, Ca2+/cAMP-response elements (CRE) or NFAT-binding elements. We found that benzyloxyphenyl NCX inhibitor KB-R7943 and SN-6, but not SEA-0400 or YM-244769 inhibited the cold induction of Per2. Our study established a real-time monitoring system for cold Ca2+ signaling which can be applied to evaluation of drugs.
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Affiliation(s)
- Hsin-tzu Wang
- grid.27476.300000 0001 0943 978XInstitute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.27476.300000 0001 0943 978XLaboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Biological Science, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Shiori Miyairi
- grid.27476.300000 0001 0943 978XInstitute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.27476.300000 0001 0943 978XLaboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Miho Kitamura
- grid.27476.300000 0001 0943 978XInstitute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.27476.300000 0001 0943 978XLaboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Kosuke Iizuka
- grid.27476.300000 0001 0943 978XInstitute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.27476.300000 0001 0943 978XLaboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Yoshimasa Asano
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Science, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Takashi Yoshimura
- grid.27476.300000 0001 0943 978XInstitute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.27476.300000 0001 0943 978XLaboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Naohiro Kon
- grid.27476.300000 0001 0943 978XInstitute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,grid.27476.300000 0001 0943 978XLaboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan ,Suntory Rising Stars Encouragement Program in Life Sciences (SunRiSE), 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto, 619-0284 Japan
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Zhang J, Dong Y, Zhou M, Wo X, Niu S, Shao E, Liu X, Jin H, Zhao W. Sulforaphane protects myocardium from ischemia-reperfusion injury by regulating CaMKIIN2 and CaMKIIδ. Biochem Biophys Res Commun 2022; 605:119-126. [DOI: 10.1016/j.bbrc.2022.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 11/02/2022]
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Zhang M, Li M, Fu H, Wang K, Tian X, Qiu R, Liu J, Gao S, Zhong Z, Yang B, Zhang L. Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1092857. [PMID: 36618608 PMCID: PMC9815118 DOI: 10.3389/fpls.2022.1092857] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/05/2022] [Indexed: 05/10/2023]
Abstract
Lonicera japonica is not only an important resource of traditional Chinese medicine, but also has very high horticultural value. Studies have been performed on the physiological responses of L. japonica leaves to chilling, however, the molecular mechanism underlying the low temperature-induced leaves morphological changes remains unclear. In this study, it has been demonstrated that the ratio of pigments content including anthocyanins, chlorophylls, and carotenoids was significantly altered in response to chilling condition, resulting in the color transformation of leaves from green to purple. Transcriptomic analysis showed there were 10,329 differentially expressed genes (DEGs) co-expressed during chilling stress. DEGs were mainly mapped to secondary metabolism, cell wall, and minor carbohydrate. The upregulated genes (UGs) were mainly enriched in protein metabolism, transport, and signaling, while UGs in secondary metabolism were mainly involved in phenylpropaoids-flavonoids pathway (PFP) and carotenoids pathway (CP). Protein-protein interaction analysis illustrated that 21 interacted genes including CAX3, NHX2, ACA8, and ACA9 were enriched in calcium transport/potassium ion transport. BR biosynthesis pathway related genes and BR insensitive (BRI) were collectively induced by chilling stress. Furthermore, the expression of genes involved in anthocyanins and CPs as well as the content of chlorogenic acid (CGA) and luteoloside were increased in leaves of L. japonica under stress. Taken together, these results indicate that the activation of PFP and CP in leaves of L. japonica under chilling stress, largely attributed to the elevation of calcium homeostasis and stimulation of BR signaling, which then regulated the PFP/CP related transcription factors.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Hongwei Fu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Kehao Wang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Xu Tian
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Renping Qiu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jinkun Liu
- Department of Techonology Center, Shandong Anran Nanometer Industry Development Company Limited, Weihai, China
| | - Shuai Gao
- Department of Techonology Center, Shandong Anran Nanometer Industry Development Company Limited, Weihai, China
| | - Zhuoheng Zhong
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bingxian Yang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- *Correspondence: Bingxian Yang, ; Lin Zhang,
| | - Lin Zhang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou, China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
- *Correspondence: Bingxian Yang, ; Lin Zhang,
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Zheng S, Su M, Wang L, Zhang T, Wang J, Xie H, Wu X, Haq SIU, Qiu QS. Small signaling molecules in plant response to cold stress. JOURNAL OF PLANT PHYSIOLOGY 2021; 266:153534. [PMID: 34601338 DOI: 10.1016/j.jplph.2021.153534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Cold stress is one of the harsh environmental stresses that adversely affect plant growth and crop yields in the Qinghai-Tibet Plateau. However, plants have evolved mechanisms to overcome the impact of cold stress. Progress has been made in understanding how plants perceive and transduce low-temperature signals to tolerate cold stress. Small signaling molecules are crucial for cellular signal transduction by initiating the downstream signaling cascade that helps plants to respond to cold stress. These small signaling molecules include calcium, reactive oxygen species, nitric oxide, hydrogen sulfide, cyclic guanosine monophosphate, phosphatidic acid, and sphingolipids. The small signaling molecules are involved in many aspects of cellular and physiological functions, such as inducing gene expression and activating hormone signaling, resulting in upregulation of the antioxidant enzyme activities, osmoprotectant accumulation, malondialdehyde reduction, and photosynthesis improvement. We summarize our current understanding of the roles of the small signaling molecules in cold stress in plants, and highlight their crosstalk in cold signaling transduction. These discoveries help us understand how the plateau plants adapt to the severe alpine environment as well as to develop new crops tolerating cold stress in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Sheng Zheng
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Min Su
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Lu Wang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Tengguo Zhang
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Juan Wang
- College of Life Sciences, Northwest Normal University, Lanzhou, 730070, China
| | - Huichun Xie
- Qinghai Provincial Key Laboratory of Medicinal Plant and Animal Resources of Qinghai-Tibet Plateau, School of Life Sciences, Qinghai Normal University, Xining, 810008, China
| | - Xuexia Wu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Syed Inzimam Ul Haq
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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