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Gabriel CH, del Olmo M, Rizki Widini A, Roshanbin R, Woyde J, Hamza E, Gutu NN, Zehtabian A, Ewers H, Granada A, Herzel H, Kramer A. Circadian period is compensated for repressor protein turnover rates in single cells. Proc Natl Acad Sci U S A 2024; 121:e2404738121. [PMID: 39141353 PMCID: PMC11348271 DOI: 10.1073/pnas.2404738121] [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: 03/06/2024] [Accepted: 07/07/2024] [Indexed: 08/15/2024] Open
Abstract
Most mammalian cells have molecular circadian clocks that generate widespread rhythms in transcript and protein abundance. While circadian clocks are robust to fluctuations in the cellular environment, little is known about the mechanisms by which the circadian period compensates for fluctuating metabolic states. Here, we exploit the heterogeneity of single cells both in circadian period and a metabolic parameter-protein stability-to study their interdependence without the need for genetic manipulation. We generated cells expressing key circadian proteins (CRYPTOCHROME1/2 (CRY1/2) and PERIOD1/2 (PER1/2)) as endogenous fusions with fluorescent proteins and simultaneously monitored circadian rhythms and degradation in thousands of single cells. We found that the circadian period compensates for fluctuations in the turnover rates of circadian repressor proteins and uncovered possible mechanisms using a mathematical model. In addition, the stabilities of the repressor proteins are circadian phase dependent and correlate with the circadian period in a phase-dependent manner, in contrast to the prevailing model.
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Affiliation(s)
- Christian H. Gabriel
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Marta del Olmo
- Institute for Theoretical Biology, Charité–Universitätsmedizin Berlin, Berlin10115, Germany
| | - Arunya Rizki Widini
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Rashin Roshanbin
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Jonas Woyde
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Ebrahim Hamza
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Nica-Nicoleta Gutu
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Berlin10117, Germany
| | - Amin Zehtabian
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin14195, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin14195, Germany
| | - Adrian Granada
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Berlin10117, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité–Universitätsmedizin Berlin, Berlin10115, Germany
| | - Achim Kramer
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
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2
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Gong S, Liang J, Xu L, Wang Y, Li J, Jin X, Yu K, Zhang Y. Diel transcriptional responses of coral-Symbiodiniaceae holobiont to elevated temperature. Commun Biol 2024; 7:882. [PMID: 39030351 PMCID: PMC11271600 DOI: 10.1038/s42003-024-06542-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 07/03/2024] [Indexed: 07/21/2024] Open
Abstract
Coral exhibits diel rhythms in behavior and gene transcription. However, the influence of elevated temperature, a key factor causing coral bleaching, on these rhythms remains poorly understood. To address this, we examined physiological, metabolic, and gene transcription oscillations in the Acropora tenuis-Cladocopium sp. holobiont under constant darkness (DD), light-dark cycle (LD), and LD with elevated temperature (HLD). Under LD, the values of photosystem II efficiency, reactive oxygen species leakage, and lipid peroxidation exhibited significant diel oscillations. These oscillations were further amplified during coral bleaching under HLD. Gene transcription analysis identified 24-hour rhythms for specific genes in both coral and Symbiodiniaceae under LD. Notably, these rhythms were disrupted in coral and shifted in Symbiodiniaceae under HLD. Importantly, we identified over 20 clock or clock-controlled genes in this holobiont. Specifically, we suggested CIPC (CLOCK-interacting pacemaker-like) gene as a core clock gene in coral. We observed that the transcription of two abundant rhythmic genes encoding glycoside hydrolases (CBM21) and heme-binding protein (SOUL) were dysregulated by elevated temperature. These findings indicate that elevated temperatures disrupt diel gene transcription rhythms in the coral-Symbiodiniaceae holobiont, affecting essential symbiosis processes, such as carbohydrate utilization and redox homeostasis. These disruptions may contribute to the thermal bleaching of coral.
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Affiliation(s)
- Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, 530004, China
| | - Lijia Xu
- South China Institute of Environmental Sciences, The Ministry of Ecology and Environment of PRC, Guangzhou, 510530, China
| | - Yongzhi Wang
- South China Institute of Environmental Sciences, The Ministry of Ecology and Environment of PRC, Guangzhou, 510530, China
| | - Jun Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Xuejie Jin
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, 530004, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| | - Yuehuan Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, China.
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3
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Schmal C. The seasons within: a theoretical perspective on photoperiodic entrainment and encoding. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:549-564. [PMID: 37659985 PMCID: PMC11226496 DOI: 10.1007/s00359-023-01669-z] [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: 03/30/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/04/2023]
Abstract
Circadian clocks are internal timing devices that have evolved as an adaption to the omnipresent natural 24 h rhythmicity of daylight intensity. Properties of the circadian system are photoperiod dependent. The phase of entrainment varies systematically with season. Plastic photoperiod-dependent re-arrangements in the mammalian circadian core pacemaker yield an internal representation of season. Output pathways of the circadian clock regulate photoperiodic responses such as flowering time in plants or hibernation in mammals. Here, we review the concepts of seasonal entrainment and photoperiodic encoding. We introduce conceptual phase oscillator models as their high level of abstraction, but, yet, intuitive interpretation of underlying parameters allows for a straightforward analysis of principles that determine entrainment characteristics. Results from this class of models are related and discussed in the context of more complex conceptual amplitude-phase oscillators as well as contextual molecular models that take into account organism, tissue, and cell-type-specific details.
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany.
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Burkart T, Willeke J, Frey E. Periodic temporal environmental variations induce coexistence in resource competition models. Phys Rev E 2023; 108:034404. [PMID: 37849086 DOI: 10.1103/physreve.108.034404] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/13/2023] [Indexed: 10/19/2023]
Abstract
Natural ecosystems, in particular on the microbial scale, are inhabited by a large number of species. The population size of each species is affected by interactions of individuals with each other and by spatial and temporal changes in environmental conditions, such as resource abundance. Here, we use a generic population dynamics model to study how, and under what conditions, a periodic temporal environmental variation can alter an ecosystem's composition and biodiversity. We demonstrate that using timescale separation allows one to qualitatively predict the long-term population dynamics of interacting species in varying environments. We show that the notion of Tilman's R* rule, a well-known principle that applies for constant environments, can be extended to periodically varying environments if the timescale of environmental changes (e.g., seasonal variations) is much faster than the timescale of population growth (doubling time in bacteria). When these timescales are similar, our analysis shows that a varying environment deters the system from reaching a steady state, and stable coexistence between multiple species becomes possible. Our results posit that biodiversity can in part be attributed to natural environmental variations.
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Affiliation(s)
- Tom Burkart
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Jan Willeke
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Theresienstraße 37, D-80333 München, Germany
- Max Planck School Matter to Life, Hofgartenstraße 8, D-80539 München, Germany
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Seki M, Ito H. Evolution of self-sustained circadian rhythms is facilitated by seasonal change of daylight. Proc Biol Sci 2022; 289:20220577. [PMID: 36416042 PMCID: PMC9682437 DOI: 10.1098/rspb.2022.0577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Self-sustained oscillation is a fundamental property of circadian rhythms and has been repeatedly tested since the early days of circadian research, resulting in the discovery of almost all organisms possessing self-sustained circadian oscillations. However, the evolutionary advantage of self-sustainability has been only speculatively discussed. In this theoretical study, we sought the environmental constraints and selection pressure that drive the acquisition or degeneration of self-sustainability through the process of evolution. We considered the dynamics of a gene regulatory network having a light input pathway under 12 h light and 12 h dark cycles or multiple day length conditions and then optimized the network structure using an evolutionary algorithm. By designing the fitness function in the evolutionary algorithm, we investigated the environmental conditions that led to the evolution of the self-sustained oscillators. Then, we found that self-sustained oscillation is rarer than damped oscillation and hourglass-type behaviour. Moreover, networks with self-sustainability have a markedly high fitness score when we assume that a network has to generate a constantly periodic expression profile regardless of day length. This study is, to our knowledge, the first to show that seasonality facilitated the evolution of the self-sustained circadian clock, which was consistent with empirical records.
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Affiliation(s)
- Motohide Seki
- Faculty of Design, Kyushu Univesity, Fukuoka 815-8540, Japan
- Institute for Asian and Oceanian Studies, Kyushu University, Fukuoka 819-0395, Japan
| | - Hiroshi Ito
- Faculty of Design, Kyushu Univesity, Fukuoka 815-8540, Japan
- Institute for Asian and Oceanian Studies, Kyushu University, Fukuoka 819-0395, Japan
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6
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Singh A, Li C, Diernfellner ACR, Höfer T, Brunner M. Data-driven modelling captures dynamics of the circadian clock of Neurospora crassa. PLoS Comput Biol 2022; 18:e1010331. [PMID: 35951637 PMCID: PMC9397904 DOI: 10.1371/journal.pcbi.1010331] [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: 03/07/2022] [Revised: 08/23/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic circadian clocks are based on self-sustaining, cell-autonomous oscillatory feedback loops that can synchronize with the environment via recurrent stimuli (zeitgebers) such as light. The components of biological clocks and their network interactions are becoming increasingly known, calling for a quantitative understanding of their role for clock function. However, the development of data-driven mathematical clock models has remained limited by the lack of sufficiently accurate data. Here we present a comprehensive model of the circadian clock of Neurospora crassa that describe free-running oscillations in constant darkness and entrainment in light-dark cycles. To parameterize the model, we measured high-resolution time courses of luciferase reporters of morning and evening specific clock genes in WT and a mutant strain. Fitting the model to such comprehensive data allowed estimating parameters governing circadian phase, period length and amplitude, and the response of genes to light cues. Our model suggests that functional maturation of the core clock protein Frequency causes a delay in negative feedback that is critical for generating circadian rhythms. Circadian rhythms are endogenous autonomous clocks that emancipate daily rhythms in physiology and behavior. Lately, a large body of research has contributed to our understanding of clocks’ genetic and mechanistic basis across kingdoms of life, i.e., mammals, fungi, plants, and bacteria. Several mathematical models have made key contributions to our current understanding of the design principles of the Neurospora crassa circadian clock and conditions for self-sustained oscillations. However, previous models uncovered and described the principle properties of the clock in generic manner due to a lack of experimental data. In this study, we developed a mathematical model based on systems of differential equations to describe the core clock components and estimated model parameters from luciferase data that capture experimental observations. We demonstrate the model predictive control simulation emphasizing the importance of functional maturation of the core clock protein Frequency in generating circadian rhythms.
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Affiliation(s)
- Amit Singh
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Congxin Li
- Theoretical Systems Biology [B086] Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | - Thomas Höfer
- Theoretical Systems Biology [B086] Deutsches Krebsforschungszentrum, Heidelberg, Germany
- * E-mail: (TH); (MB)
| | - Michael Brunner
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (TH); (MB)
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Abstract
Sunlight drives phototrophic metabolism, which affects redox conditions and produces substrates for nonphototrophs. These environmental parameters fluctuate daily due to Earth’s rotation, and nonphototrophic organisms can therefore benefit from the ability to respond to, or even anticipate, such changes. Circadian rhythms, such as daily changes in body temperature, in host organisms can also affect local conditions for colonizing bacteria. Here, we investigated the effects of light/dark and temperature cycling on biofilms of the opportunistic pathogen Pseudomonas aeruginosa PA14. We grew biofilms in the presence of a respiratory indicator dye and found that enhanced dye reduction occurred in biofilm zones that formed during dark intervals and at lower temperatures. This pattern formation occurred with cycling of blue, red, or far-red light, and a screen of mutants representing potential sensory proteins identified two with defects in pattern formation, specifically under red light cycling. We also found that the physiological states of biofilm subzones formed under specific light and temperature conditions were retained during subsequent condition cycling. Light/dark and temperature cycling affected expression of genes involved in primary metabolic pathways and redox homeostasis, including those encoding electron transport chain components. Consistent with this, we found that cbb3-type oxidases contribute to dye reduction under light/dark cycling conditions. Together, our results indicate that cyclic changes in light exposure and temperature have lasting effects on redox metabolism in biofilms formed by a nonphototrophic, pathogenic bacterium.
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Khan E, Saghafi S, Diekman CO, Rotstein HG. The emergence of polyglot entrainment responses to periodic inputs in vicinities of Hopf bifurcations in slow-fast systems. CHAOS (WOODBURY, N.Y.) 2022; 32:063137. [PMID: 35778129 DOI: 10.1063/5.0079198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Several distinct entrainment patterns can occur in the FitzHugh-Nagumo (FHN) model under external periodic forcing. Investigating the FHN model under different types of periodic forcing reveals the existence of multiple disconnected 1:1 entrainment segments for constant, low enough values of the input amplitude when the unforced system is in the vicinity of a Hopf bifurcation. This entrainment structure is termed polyglot to distinguish it from the single 1:1 entrainment region (monoglot) structure typically observed in Arnold tongue diagrams. The emergence of polyglot entrainment is then explained using phase-plane analysis and other dynamical system tools. Entrainment results are investigated for other slow-fast systems of neuronal, circadian, and glycolytic oscillations. Exploring these models, we found that polyglot entrainment structure (multiple 1:1 regions) is observed when the unforced system is in the vicinity of a Hopf bifurcation and the Hopf point is located near a knee of a cubic-like nullcline.
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Affiliation(s)
- Emel Khan
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Soheil Saghafi
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Casey O Diekman
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Horacio G Rotstein
- Federated Department of Biological Sciences, New Jersey Institute of Technology & Rutgers University, Newark, New Jersey 07102, USA
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Schmal C, Hong S, Tokuda IT, Myung J. Editorial: Coupling in biological systems: Definitions, mechanisms, and implications. FRONTIERS IN NETWORK PHYSIOLOGY 2022; 2:1076702. [PMID: 36926102 PMCID: PMC10012964 DOI: 10.3389/fnetp.2022.1076702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt University, Berlin, Germany
| | - Sungho Hong
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Isao T Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Shiga, Japan
| | - Jihwan Myung
- Graduate Institute of Mind, Brain and Consciousness (GIMBC), Taipei Medical University, Taipei, Taiwan.,Brain and Consciousness Research Centre (BCRC), TMU-Shuang Ho Hospital, New Taipei City, Taiwan
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