1
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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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2
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Tyler J, Lu Y, Dunlap J, Forger DB. Evolution of the repression mechanisms in circadian clocks. Genome Biol 2022; 23:17. [PMID: 35012616 PMCID: PMC8751359 DOI: 10.1186/s13059-021-02571-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/07/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Circadian (daily) timekeeping is essential to the survival of many organisms. An integral part of all circadian timekeeping systems is negative feedback between an activator and repressor. However, the role of this feedback varies widely between lower and higher organisms. RESULTS Here, we study repression mechanisms in the cyanobacterial and eukaryotic clocks through mathematical modeling and systems analysis. We find a common mathematical model that describes the mechanism by which organisms generate rhythms; however, transcription's role in this has diverged. In cyanobacteria, protein sequestration and phosphorylation generate and regulate rhythms while transcription regulation keeps proteins in proper stoichiometric balance. Based on recent experimental work, we propose a repressor phospholock mechanism that models the negative feedback through transcription in clocks of higher organisms. Interestingly, this model, when coupled with activator phosphorylation, allows for oscillations over a wide range of protein stoichiometries, thereby reconciling the negative feedback mechanism in Neurospora with that in mammals and cyanobacteria. CONCLUSIONS Taken together, these results paint a picture of how circadian timekeeping may have evolved.
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Affiliation(s)
- Jonathan Tyler
- Department of Mathematics, University of Michigan, Ann Arbor, 48109 MI USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Michigan, Ann Arbor, 48109 MI USA
| | - Yining Lu
- Department of Mathematics, University of Michigan, Ann Arbor, 48109 MI USA
| | - Jay Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, 03755 NH USA
| | - Daniel B. Forger
- Department of Mathematics, University of Michigan, Ann Arbor, 48109 MI USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, 48109 MI USA
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3
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Abstract
Circadian clocks are autonomous systems able to oscillate in a self-sustained manner in the absence of external cues, although such Zeitgebers are typically present. At the cellular level, the molecular clockwork consists of a complex network of interlocked feedback loops. This chapter discusses self-sustained circadian oscillators in the context of nonlinear dynamics theory. We suggest basic steps that can help in constructing a mathematical model and introduce how self-sustained generations can be modeled using ordinary differential equations. Moreover, we discuss how coupled oscillators synchronize among themselves or entrain to periodic signals. The development of mathematical models over the last years has helped to understand such complex network systems and to highlight the basic building blocks in which oscillating systems are built upon. We argue that, through theoretical predictions, the use of simple models can guide experimental research and is thus suitable to model biological systems qualitatively.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, Berlin, Germany.
| | - Saskia Grabe
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité and Humboldt Universität zu Berlin, Berlin, Germany
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4
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Burt P, Grabe S, Madeti C, Upadhyay A, Merrow M, Roenneberg T, Herzel H, Schmal C. Principles underlying the complex dynamics of temperature entrainment by a circadian clock. iScience 2021; 24:103370. [PMID: 34816105 PMCID: PMC8593569 DOI: 10.1016/j.isci.2021.103370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/01/2021] [Accepted: 10/25/2021] [Indexed: 01/20/2023] Open
Abstract
Autonomously oscillating circadian clocks resonate with daily environmental (zeitgeber) rhythms to organize physiology around the solar day. Although entrainment properties and mechanisms have been studied widely and in great detail for light-dark cycles, entrainment to daily temperature rhythms remains poorly understood despite that they are potent zeitgebers. Here we investigate the entrainment of the chronobiological model organism Neurospora crassa, subject to thermocycles of different periods and fractions of warm versus cold phases, mimicking seasonal variations. Depending on the properties of these thermocycles, regularly entrained rhythms, period-doubling (frequency demultiplication) but also irregular aperiodic behavior occurs. We demonstrate that the complex nonlinear phenomena of experimentally observed entrainment dynamics can be understood by molecular mathematical modeling.
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Affiliation(s)
- Philipp Burt
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Saskia Grabe
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Cornelia Madeti
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Abhishek Upadhyay
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Till Roenneberg
- Institute of Medical Psychology, Faculty of Medicine, LMU Munich, Goethestrasse 31, 80336 Munich, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology, Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
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5
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Upadhyay A, Marzoll D, Diernfellner A, Brunner M, Herzel H. Multiple random phosphorylations in clock proteins provide long delays and switches. Sci Rep 2020; 10:22224. [PMID: 33335302 PMCID: PMC7746754 DOI: 10.1038/s41598-020-79277-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/25/2020] [Indexed: 12/27/2022] Open
Abstract
Theory predicts that self-sustained oscillations require robust delays and nonlinearities (ultrasensitivity). Delayed negative feedback loops with switch-like inhibition of transcription constitute the core of eukaryotic circadian clocks. The kinetics of core clock proteins such as PER2 in mammals and FRQ in Neurospora crassa is governed by multiple phosphorylations. We investigate how multiple, slow and random phosphorylations control delay and molecular switches. We model phosphorylations of intrinsically disordered clock proteins (IDPs) using conceptual models of sequential and distributive phosphorylations. Our models help to understand the underlying mechanisms leading to delays and ultrasensitivity. The model shows temporal and steady state switches for the free kinase and the phosphoprotein. We show that random phosphorylations and sequestration mechanisms allow high Hill coefficients required for self-sustained oscillations.
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Affiliation(s)
- Abhishek Upadhyay
- Institute for Theoretical Biology, Charité, Universitätsmedizin Berlin, Humboldt University of Berlin, Philippstr. 13, 10115, Berlin, Germany.
| | - Daniela Marzoll
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Axel Diernfellner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Michael Brunner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité, Universitätsmedizin Berlin, Humboldt University of Berlin, Philippstr. 13, 10115, Berlin, Germany.
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6
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Schmal C, Herzel H, Myung J. Clocks in the Wild: Entrainment to Natural Light. Front Physiol 2020; 11:272. [PMID: 32300307 PMCID: PMC7142224 DOI: 10.3389/fphys.2020.00272] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/09/2020] [Indexed: 01/09/2023] Open
Abstract
Entrainment denotes a process of coordinating the internal circadian clock to external rhythmic time-cues (Zeitgeber), mainly light. It is facilitated by stronger Zeitgeber signals and smaller period differences between the internal clock and the external Zeitgeber. The phase of entrainment ψ is a result of this process on the side of the circadian clock. On Earth, the period of the day-night cycle is fixed to 24 h, while the periods of circadian clocks distribute widely due to natural variation within and between species. The strength and duration of light depend locally on season and geographic latitude. Therefore, entrainment characteristics of a circadian clock vary under a local light environment and distribute along geoecological settings. Using conceptual models of circadian clocks, we investigate how local conditions of natural light shape global patterning of entrainment through seasons. This clock-side entrainment paradigm enables us to predict systematic changes in the global distribution of chronotypes.
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Affiliation(s)
- Christoph Schmal
- Department of Biology, Faculty of Life Sciences, Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Department Basic Sciences, Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jihwan Myung
- Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan.,Brain and Consciousness Research Centre, Taipei Medical University-Shuang Ho Hospital, Ministry of Health and Welfare, New Taipei City, Taiwan.,Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan.,Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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7
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Schmal C, Ono D, Myung J, Pett JP, Honma S, Honma KI, Herzel H, Tokuda IT. Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics. PLoS Comput Biol 2019; 15:e1007330. [PMID: 31513579 PMCID: PMC6759184 DOI: 10.1371/journal.pcbi.1007330] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/24/2019] [Accepted: 08/12/2019] [Indexed: 01/11/2023] Open
Abstract
Circadian rhythms are generated by interlocked transcriptional-translational negative feedback loops (TTFLs), the molecular process implemented within a cell. The contributions, weighting and balancing between the multiple feedback loops remain debated. Dissociated, free-running dynamics in the expression of distinct clock genes has been described in recent experimental studies that applied various perturbations such as slice preparations, light pulses, jet-lag, and culture medium exchange. In this paper, we provide evidence that this "presumably transient" dissociation of circadian gene expression oscillations may occur at the single-cell level. Conceptual and detailed mechanistic mathematical modeling suggests that such dissociation is due to a weak interaction between multiple feedback loops present within a single cell. The dissociable loops provide insights into underlying mechanisms and general design principles of the molecular circadian clock.
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Affiliation(s)
- Christoph Schmal
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Daisuke Ono
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Jihwan Myung
- Laboratory of Braintime, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Brain and Consciousness, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - J. Patrick Pett
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Sato Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ken-Ichi Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isao T. Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
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8
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Upadhyay A, Brunner M, Herzel H. An Inactivation Switch Enables Rhythms in a Neurospora Clock Model. Int J Mol Sci 2019; 20:E2985. [PMID: 31248072 PMCID: PMC6627049 DOI: 10.3390/ijms20122985] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/14/2019] [Accepted: 06/15/2019] [Indexed: 12/17/2022] Open
Abstract
Autonomous endogenous time-keeping is ubiquitous across many living organisms, known as the circadian clock when it has a period of about 24 h. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungus Neurospora crassa is a well-established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock of Neurospora is composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex, which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics, we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedback among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 h. Our model reveals a switch between WC1-induced transcription and FFC-assisted inactivation of WC1. Using the new model, we also study the possible mechanisms of glucose compensation. A fairly simple model with just three nonlinearities helps to elucidate clock dynamics, revealing a mechanism of rhythms' production. The model can further be utilized to study entrainment and temperature compensation.
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Affiliation(s)
- Abhishek Upadhyay
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin and Humboldt University of Berlin, Philippstr. 13, 10115 Berlin, Germany.
| | - Michael Brunner
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité-Universitätsmedizin Berlin and Humboldt University of Berlin, Philippstr. 13, 10115 Berlin, Germany.
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9
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Modeling the crosstalk between the circadian clock and ROS in Neurospora crassa. J Theor Biol 2018; 458:125-132. [DOI: 10.1016/j.jtbi.2018.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/19/2018] [Accepted: 09/13/2018] [Indexed: 11/18/2022]
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10
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Ultradian Rhythms in the Transcriptome of Neurospora crassa. iScience 2018; 9:475-486. [PMID: 30472532 PMCID: PMC6260400 DOI: 10.1016/j.isci.2018.11.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 07/30/2018] [Accepted: 11/05/2018] [Indexed: 11/22/2022] Open
Abstract
In many organisms, the circadian clock drives rhythms in the transcription of clock-controlled genes that can be either circadian (∼24-hr period) or ultradian (<24-hr period). Ultradian rhythms with periods that are a fraction of 24 hr are termed harmonics. Several harmonic transcripts were discovered in the mouse liver, but their functional significance remains unclear. Using a model-based analysis, we report for the first time ∼7-hr third harmonic transcripts in Neurospora crassa, a well-established fungal circadian model organism. Several third harmonic genes are regulated by female fertility 7 (FF-7), whose transcript itself is third harmonic. The knockout of circadian output regulator CSP1 superimposes circadian rhythms on the third harmonic genes, whereas the knockout of stress response regulator MSN1 converts third harmonic rhythms to second harmonic rhythms. The 460 ∼7-hr genes are co-regulated in two anti-phasic groups in multiple genotypes and include kinases, chromatin remodelers, and homologs of harmonic genes in the mouse liver. Coexisting harmonic ∼7-hr and circadian rhythms in fungal clock model organism Knockout of output regulator CSP1 imposes circadian rhythms over ∼7-hr rhythms Third harmonic rhythms are a part of key cellular processes and mediated by FF-7 7-hr genes are co-regulated in two anti-phasic clusters across genotypes and laboratories
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11
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Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock. Biophys J 2018; 115:2055-2066. [PMID: 30473017 DOI: 10.1016/j.bpj.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/29/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
Mathematical models of fundamental biological processes play an important role in consolidating theory and experiments, especially if they are systematically developed, thoroughly characterized, and well tested by experimental data. In this work, we report a detailed bifurcation analysis of a mathematical model of the mammalian circadian clock network developed by Relógio et al., noteworthy for its consistency with available data. Using one- and two-parameter bifurcation diagrams, we explore how oscillations in the model depend on the expression levels of its constituent genes and the activities of their encoded proteins. These bifurcation diagrams allow us to decipher the dynamics of interlocked feedback loops by parametric variation of genes and proteins in the model. Among other results, we find that REV-ERB, a member of a subfamily of orphan nuclear receptors, plays a critical role in the intertwined dynamics of Relógio's model. The bifurcation diagrams reported here can be used for predicting how the core clock network responds-in terms of period, amplitude and phases of oscillations-to different perturbations.
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12
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Foo M, Somers DE, Kim PJ. Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System. PLoS Comput Biol 2016; 12:e1004748. [PMID: 26828650 PMCID: PMC4734688 DOI: 10.1371/journal.pcbi.1004748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/11/2016] [Indexed: 02/03/2023] Open
Abstract
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear that plants harbor more complex gene regulatory circuits within the core circadian clocks than other organisms, inspiring a fundamental question: are all these regulatory interactions between clock genes equally crucial for the establishment and maintenance of circadian rhythms? Our mechanistic simulation for Arabidopsis thaliana demonstrates that at least half of the total regulatory interactions must be present to express the circadian molecular profiles observed in wild-type plants. A set of those essential interactions is called herein a kernel of the circadian system. The kernel structure unbiasedly reveals four interlocked negative feedback loops contributing to circadian rhythms, and three feedback loops among them drive the autonomous oscillation itself. Strikingly, the kernel structure, as well as the whole clock circuitry, is overwhelmingly composed of inhibitory, rather than activating, interactions between genes. We found that this tendency underlies plant circadian molecular profiles which often exhibit sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate profiles, inhibitory interactions may facilitate the global coordination of temporally-distant clock events that are markedly peaked at very specific times of day. Our systematic approach resulting in experimentally-testable predictions provides insights into a design principle of biological clockwork, with implications for synthetic biology.
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Affiliation(s)
- Mathias Foo
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, Republic of Korea
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - David E. Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Pan-Jun Kim
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, Republic of Korea
- Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
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13
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Dovzhenok AA, Baek M, Lim S, Hong CI. Mathematical modeling and validation of glucose compensation of the neurospora circadian clock. Biophys J 2016; 108:1830-1839. [PMID: 25863073 DOI: 10.1016/j.bpj.2015.01.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/05/2014] [Accepted: 01/09/2015] [Indexed: 11/26/2022] Open
Abstract
Autonomous circadian oscillations arise from transcriptional-translational feedback loops of core clock components. The period of a circadian oscillator is relatively insensitive to changes in nutrients (e.g., glucose), which is referred to as "nutrient compensation". Recently, a transcription repressor, CSP-1, was identified as a component of the circadian system in Neurospora crassa. The transcription of csp-1 is under the circadian regulation. Intriguingly, CSP-1 represses the circadian transcription factor, WC-1, forming a negative feedback loop that can influence the core oscillator. This feedback mechanism is suggested to maintain the circadian period in a wide range of glucose concentrations. In this report, we constructed a mathematical model of the Neurospora circadian clock incorporating the above WC-1/CSP-1 feedback loop, and investigated molecular mechanisms of glucose compensation. Our model shows that glucose compensation exists within a narrow range of parameter space where the activation rates of csp-1 and wc-1 are balanced with each other, and simulates loss of glucose compensation in csp-1 mutants. More importantly, we experimentally validated rhythmic oscillations of the wc-1 gene expression and loss of glucose compensation in the wc-1(ov) mutant as predicted in the model. Furthermore, our stochastic simulations demonstrate that the CSP-1-dependent negative feedback loop functions in glucose compensation, but does not enhance the overall robustness of oscillations against molecular noise. Our work highlights predictive modeling of circadian clock machinery and experimental validations employing Neurospora and brings a deeper understanding of molecular mechanisms of glucose compensation.
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Affiliation(s)
- Andrey A Dovzhenok
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Mokryun Baek
- Department of Molecular and Cellular Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Sookkyung Lim
- Department of Mathematical Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati College of Medicine, Cincinnati, Ohio.
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14
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Proietto M, Bianchi MM, Ballario P, Brenna A. Epigenetic and Posttranslational Modifications in Light Signal Transduction and the Circadian Clock in Neurospora crassa. Int J Mol Sci 2015; 16:15347-83. [PMID: 26198228 PMCID: PMC4519903 DOI: 10.3390/ijms160715347] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/24/2015] [Accepted: 06/30/2015] [Indexed: 12/15/2022] Open
Abstract
Blue light, a key abiotic signal, regulates a wide variety of physiological processes in many organisms. One of these phenomena is the circadian rhythm presents in organisms sensitive to the phase-setting effects of blue light and under control of the daily alternation of light and dark. Circadian clocks consist of autoregulatory alternating negative and positive feedback loops intimately connected with the cellular metabolism and biochemical processes. Neurospora crassa provides an excellent model for studying the molecular mechanisms involved in these phenomena. The White Collar Complex (WCC), a blue-light receptor and transcription factor of the circadian oscillator, and Frequency (FRQ), the circadian clock pacemaker, are at the core of the Neurospora circadian system. The eukaryotic circadian clock relies on transcriptional/translational feedback loops: some proteins rhythmically repress their own synthesis by inhibiting the activity of their transcriptional factors, generating self-sustained oscillations over a period of about 24 h. One of the basic mechanisms that perpetuate self-sustained oscillations is post translation modification (PTM). The acronym PTM generically indicates the addition of acetyl, methyl, sumoyl, or phosphoric groups to various types of proteins. The protein can be regulatory or enzymatic or a component of the chromatin. PTMs influence protein stability, interaction, localization, activity, and chromatin packaging. Chromatin modification and PTMs have been implicated in regulating circadian clock function in Neurospora. Research into the epigenetic control of transcription factors such as WCC has yielded new insights into the temporal modulation of light-dependent gene transcription. Here we report on epigenetic and protein PTMs in the regulation of the Neurospora crassa circadian clock. We also present a model that illustrates the molecular mechanisms at the basis of the blue light control of the circadian clock.
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Affiliation(s)
- Marco Proietto
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Michele Maria Bianchi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Paola Ballario
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Pasteur Institute, Cenci Bolognetti Foundation and Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
| | - Andrea Brenna
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Pasteur Institute, Cenci Bolognetti Foundation and Department of Biology and Biotechnology "Charles Darwin", Sapienza-University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy.
- Department of Biology, Division of Biochemistry, University of Fribourg, Chemin du Musée 5, Fribourg 1700, Switzerland.
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15
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Henson MA. Understanding environmental adaptation of the fungal circadian clock with mathematical modeling. Biophys J 2015; 108:1580-1582. [PMID: 25863047 DOI: 10.1016/j.bpj.2015.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 02/18/2015] [Indexed: 10/23/2022] Open
Affiliation(s)
- Michael A Henson
- Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts.
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16
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Xue Z, Ye Q, Anson SR, Yang J, Xiao G, Kowbel D, Glass NL, Crosthwaite SK, Liu Y. Transcriptional interference by antisense RNA is required for circadian clock function. Nature 2014; 514:650-3. [PMID: 25132551 PMCID: PMC4214883 DOI: 10.1038/nature13671] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 07/10/2014] [Indexed: 01/24/2023]
Abstract
Eukaryotic circadian oscillators consist of negative feedback loops that generate endogenous rhythmicities1. Natural antisense RNAs are found in a wide range of eukaryotic organisms2-5. Nevertheless, the physiological importance and mode of action of most antisense RNAs is not clear6-9. frequency (frq) encodes a component of the Neurospora core circadian negative feedback loop which was thought to generate sustained rhythmicity10. Transcription of qrf, the long non-coding frq antisense RNA, is light induced, and its level oscillates in antiphase to frq sense RNA3. Here we show that qrf transcription is regulated by both light-dependent and -independent mechanisms. Light-dependent qrf transcription represses frq expression and regulates clock resetting. qrf expression in the dark, on the other hand, is required for circadian rhythmicity. frq transcription also inhibits qrf expression and surprisingly, drives the antiphasic rhythm of qrf transcripts. The mutual inhibition of frq and qrf transcription thus forms a double negative feedback loop that is interlocked with the core feedback loop. Genetic and mathematical modeling analyses indicate that such an arrangement is required for robust and sustained circadian rhythmicity. Moreover, our results suggest that antisense transcription inhibits sense expression by mediating chromatin modifications and premature transcription termination. Together, our results established antisense transcription as an essential feature in a circadian system and shed light on the importance and mechanism of antisense action.
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Affiliation(s)
- Zhihong Xue
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Qiaohong Ye
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Simon R Anson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Jichen Yang
- Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - Guanghua Xiao
- Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
| | - David Kowbel
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - N Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | | | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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17
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Akman OE, Watterson S, Parton A, Binns N, Millar AJ, Ghazal P. Digital clocks: simple Boolean models can quantitatively describe circadian systems. J R Soc Interface 2012; 9:2365-82. [PMID: 22499125 PMCID: PMC3405750 DOI: 10.1098/rsif.2012.0080] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. The clock functions by generating endogenous rhythms that can be entrained to the external 24-h day–night cycle, enabling organisms to optimally time biochemical processes relative to dawn and dusk. In recent years, computational models based on differential equations have become useful tools for dissecting and quantifying the complex regulatory relationships underlying the clock's oscillatory dynamics. However, optimizing the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of in silico studies. Here, we develop an approach based on Boolean logic that dramatically reduces the parametrization, making the state and parameter spaces finite and tractable. We introduce efficient methods for fitting Boolean models to molecular data, successfully demonstrating their application to synthetic time courses generated by a number of established clock models, as well as experimental expression levels measured using luciferase imaging. Our results indicate that despite their relative simplicity, logic models can (i) simulate circadian oscillations with the correct, experimentally observed phase relationships among genes and (ii) flexibly entrain to light stimuli, reproducing the complex responses to variations in daylength generated by more detailed differential equation formulations. Our work also demonstrates that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. By presenting the first Boolean models of circadian circuits together with general techniques for their optimization, we hope to establish a new framework for the systematic modelling of more complex clocks, as well as other circuits with different qualitative dynamics. In particular, we anticipate that the ability of logic models to provide a computationally efficient representation of system behaviour could greatly facilitate the reverse-engineering of large-scale biochemical networks.
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Affiliation(s)
- Ozgur E Akman
- Centre for Systems, Dynamics and Control, College of Engineering, Computing and Mathematics, University of Exeter, Exeter, UK.
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18
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Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM. Comprehensive modelling of the Neurospora circadian clock and its temperature compensation. PLoS Comput Biol 2012; 8:e1002437. [PMID: 22496627 PMCID: PMC3320131 DOI: 10.1371/journal.pcbi.1002437] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/06/2012] [Indexed: 11/19/2022] Open
Abstract
Circadian clocks provide an internal measure of external time allowing organisms to anticipate and exploit predictable daily changes in the environment. Rhythms driven by circadian clocks have a temperature compensated periodicity of approximately 24 hours that persists in constant conditions and can be reset by environmental time cues. Computational modelling has aided our understanding of the molecular mechanisms of circadian clocks, nevertheless it remains a major challenge to integrate the large number of clock components and their interactions into a single, comprehensive model that is able to account for the full breadth of clock phenotypes. Here we present a comprehensive dynamic model of the Neurospora crassa circadian clock that incorporates its key components and their transcriptional and post-transcriptional regulation. The model accounts for a wide range of clock characteristics including: a periodicity of 21.6 hours, persistent oscillation in constant conditions, arrhythmicity in constant light, resetting by brief light pulses, and entrainment to full photoperiods. Crucial components influencing the period and amplitude of oscillations were identified by control analysis. Furthermore, simulations enabled us to propose a mechanism for temperature compensation, which is achieved by simultaneously increasing the translation of frq RNA and decreasing the nuclear import of FRQ protein. Circadian clocks are internal timekeepers that integrate signals from the environment and orchestrate cellular events to occur at the most favourable time of day. Circadian clocks in animals, plants, fungi and bacteria have similar characteristic properties and molecular architecture. They have a periodicity of approximately 24 hours, persist in constant conditions and can be reset by environmental time cues such as light and temperature. Another essential property, whose molecular basis is poorly understood, is that the period is temperature compensated i.e. it remains the same over a range of temperatures. Computational modelling has become a valuable tool to predict and understand the underlying mechanisms of such complex molecular systems, but existing clock models are often restricted in the scope of molecular reactions they cover and in the breadth of conditions they are able to reproduce. We therefore built a comprehensive model of the circadian clock of the fungus Neurospora crassa, which encompasses existing knowledge of the biochemistry of the Neurospora clock. We validated this model against a wide range of experimental phenotypes and then used the model to investigate possible molecular explanations of temperature compensation. Our simulations suggest that temperature compensation of period is achieved by changing the abundance and cellular localisation of a key clock protein.
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Affiliation(s)
- Yu-Yao Tseng
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Suzanne M. Hunt
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Christian Heintzen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Susan K. Crosthwaite
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail: (SKC); (JMS)
| | - Jean-Marc Schwartz
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail: (SKC); (JMS)
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19
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Miró-Bueno JM, Rodríguez-Patón A. A simple negative interaction in the positive transcriptional feedback of a single gene is sufficient to produce reliable oscillations. PLoS One 2011; 6:e27414. [PMID: 22205920 PMCID: PMC3244268 DOI: 10.1371/journal.pone.0027414] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/17/2011] [Indexed: 11/19/2022] Open
Abstract
Negative and positive transcriptional feedback loops are present in natural and synthetic genetic oscillators. A single gene with negative transcriptional feedback needs a time delay and sufficiently strong nonlinearity in the transmission of the feedback signal in order to produce biochemical rhythms. A single gene with only positive transcriptional feedback does not produce oscillations. Here, we demonstrate that this single-gene network in conjunction with a simple negative interaction can also easily produce rhythms. We examine a model comprised of two well-differentiated parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the dynamics of the oscillator are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this paper is that a simple and usual negative interaction, such as degradation, sequestration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. This means that at the genetic level an explicit negative feedback loop is not necessary. The model needs neither cooperative binding reactions nor the formation of protein multimers. Therefore, our findings could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators.
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Affiliation(s)
- Jesús M. Miró-Bueno
- Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
- * E-mail: (JMMB); (ARP)
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain
- * E-mail: (JMMB); (ARP)
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20
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Jolma IW, Laerum OD, Lillo C, Ruoff P. Circadian oscillators in eukaryotes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:533-549. [PMID: 20836046 DOI: 10.1002/wsbm.81] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The biological clock, present in nearly all eukaryotes, has evolved such that organisms can adapt to our planet's rotation in order to anticipate the coming day or night as well as unfavorable seasons. As all modern high-precision chronometers, the biological clock uses oscillation as a timekeeping element. In this review, we describe briefly the discovery, historical development, and general properties of circadian oscillators. The issue of temperature compensation (TC) is discussed, and our present understanding of the underlying genetic and biochemical mechanisms in circadian oscillators are described with special emphasis on Neurospora crassa, mammals, and plants.
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Affiliation(s)
- Ingunn W Jolma
- Centre of Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Ole Didrik Laerum
- The Gade Institute, Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Cathrine Lillo
- Centre of Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Peter Ruoff
- Centre of Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
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21
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Akman OE, Rand DA, Brown PE, Millar AJ. Robustness from flexibility in the fungal circadian clock. BMC SYSTEMS BIOLOGY 2010; 4:88. [PMID: 20576110 PMCID: PMC2913929 DOI: 10.1186/1752-0509-4-88] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 06/24/2010] [Indexed: 12/01/2022]
Abstract
Background Robustness is a central property of living systems, enabling function to be maintained against environmental perturbations. A key challenge is to identify the structures in biological circuits that confer system-level properties such as robustness. Circadian clocks allow organisms to adapt to the predictable changes of the 24-hour day/night cycle by generating endogenous rhythms that can be entrained to the external cycle. In all organisms, the clock circuits typically comprise multiple interlocked feedback loops controlling the rhythmic expression of key genes. Previously, we showed that such architectures increase the flexibility of the clock's rhythmic behaviour. We now test the relationship between flexibility and robustness, using a mathematical model of the circuit controlling conidiation in the fungus Neurospora crassa. Results The circuit modelled in this work consists of a central negative feedback loop, in which the frequency (frq) gene inhibits its transcriptional activator white collar-1 (wc-1), interlocked with a positive feedback loop in which FRQ protein upregulates WC-1 production. Importantly, our model reproduces the observed entrainment of this circuit under light/dark cycles with varying photoperiod and cycle duration. Our simulations show that whilst the level of frq mRNA is driven directly by the light input, the falling phase of FRQ protein, a molecular correlate of conidiation, maintains a constant phase that is uncoupled from the times of dawn and dusk. The model predicts the behaviour of mutants that uncouple WC-1 production from FRQ's positive feedback, and shows that the positive loop enhances the buffering of conidiation phase against seasonal photoperiod changes. This property is quantified using Kitano's measure for the overall robustness of a regulated system output. Further analysis demonstrates that this functional robustness is a consequence of the greater evolutionary flexibility conferred on the circuit by the interlocking loop structure. Conclusions Our model shows that the behaviour of the fungal clock in light-dark cycles can be accounted for by a transcription-translation feedback model of the central FRQ-WC oscillator. More generally, we provide an example of a biological circuit in which greater flexibility yields improved robustness, while also introducing novel sensitivity analysis techniques applicable to a broader range of cellular oscillators.
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Affiliation(s)
- Ozgur E Akman
- Centre for Systems Biology at Edinburgh, The University of Edinburgh, Edinburgh, UK
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22
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Cheng Z, Liu F, Zhang XP, Wang W. Reversible phosphorylation subserves robust circadian rhythms by creating a switch in inactivating the positive element. Biophys J 2010; 97:2867-75. [PMID: 19948115 DOI: 10.1016/j.bpj.2009.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 09/02/2009] [Accepted: 09/03/2009] [Indexed: 11/28/2022] Open
Abstract
Reversible phosphorylation of proteins is ubiquitous in circadian systems, but the role it plays in generating rhythmicity is not completely understood. A common mechanism for most circadian rhythms involves a negative feedback loop between the positive and negative elements. Here, we built a minimal model for the Neurospora crassa circadian clock based on the core negative feedback loop and the protein FREQUENCY (FRQ)-dependent phosphorylation of the White Collar Complex (WCC). The model can reproduce basic features of the clock, such as the period length, phase relationship, and entrainment to light/dark cycles. We found that the activity of WCC can be controlled by FRQ in a switchlike manner owing to zero-order ultrasensitivity. WCC is inactivated when FRQ level crosses a threshold from below. As a result, low cooperativity in transcriptional activation is sufficient for circadian rhythms, and the level of active WCC exhibits spiky oscillations. Such oscillations are robust to molecular noise and may subserve controlling circadian output. Therefore, the core negative feedback together with phosphorylation of the positive element can ensure robust circadian rhythms. Our work provides insights into the critical roles of posttranslational modification in circadian clocks.
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Affiliation(s)
- Zhang Cheng
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing, China
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23
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Hong CI, Ruoff P, Loros JJ, Dunlap JC. Closing the circadian negative feedback loop: FRQ-dependent clearance of WC-1 from the nucleus. Genes Dev 2008; 22:3196-204. [PMID: 18997062 DOI: 10.1101/gad.1706908] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In Neurospora crassa, a transcription factor, WCC, activates the transcription of frq. FRQ forms homodimers as well as complexes with an RNA helicase, FRH, and the WCC, and translocates into the nucleus to inactivate the WCC, closing the time-delayed negative feedback loop. The detailed mechanism for closing this loop, however, remains incompletely understood. In particular within the nucleus, the low amount of FRQ compared with that of WC-1 creates a conundrum: How can the nuclear FRQ inactivate the larger amount of WCC? One possibility is that FRQ might function as a catalytic component in phosphorylation-dependent inhibition. However, in silico experiments reveal that stoichiometric noncatalytic binding and inhibition can generate a robust oscillator, even when nuclear FRQ levels are substantially lower than nuclear WCC, so long as there is FRQ-dependent clearance of WC-1 from the nucleus. Based on this model, we can predict and now demonstrate that WC-1 stability cycles, that WC-1 is stable in the absence of FRQ, and that physical binding between FRQ and WCC is essential for closure of the negative feedback loop. Moreover, and consistent with a noncatalytic clearance-based model for inhibition, appreciable amounts of the nuclear FRQ:WCC complex accumulate at some times of day, comprising as much as 10% of the nuclear WC-1.
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Affiliation(s)
- Christian I Hong
- Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
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