Dataset Information

Akman2008_Circadian_Clock_Model1

ABSTRACT: This a model from the article: Isoform switching facilitates period control in the Neurospora crassa circadian clock. Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA Mol. Syst. Biol. 2008;Vol 4: 164 18277380 , Abstract: A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neurospora crassa circadian network incorporating experimental work showing that temperature alters the balance of translation between a short and long form of the FREQUENCY (FRQ) protein. This is used to discuss period control and functionality for the Neurospora system. The model reproduces a broad range of key experimental data on temperature dependence and rhythmicity, both in wild-type and mutant strains. We present a simple mechanism utilising the presence of the FRQ isoforms (isoform switching) by which period control could have evolved, and argue that this regulatory structure may also increase the temperature range where the clock is robustly rhythmic. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. For more information see the terms of use . To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

SUBMITTER: Lukas Endler

PROVIDER: BIOMD0000000295 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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			Action	DRS
	BIOMD0000000295?filename=BIOMD0000000295-biopax2.owl	Owl
	BIOMD0000000295?filename=BIOMD0000000295-biopax3.owl	Owl
	BIOMD0000000295?filename=BIOMD0000000295-matlab.m	Other
	BIOMD0000000295?filename=BIOMD0000000295-octave.m	Other
	BIOMD0000000295?filename=BIOMD0000000295.m	Other

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Isoform switching facilitates period control in the Neurospora crassa circadian clock.

Akman Ozgur E OE Locke James C W JC Tang Sanyi S Carré Isabelle I Millar Andrew J AJ Rand David A DA

Molecular systems biology 20080212

A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neu ...[more]

PMID: 18277380

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Project description:This model 2 described in the supplement of the article below. It is parameterized for the WT at 24°C. To reproduce figure 6 the results have to be rescaled to circadian time by multiplying time by 24/tau, with tau being the period of the free-running oscillator. For the wild-type parameter set tau is equal to 22.7149. Article: Isoform switching facilitates period control in the Neurospora crassa circadian clock. Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA. Mol Syst Biol. 2008;4:164. Epub 2008 Feb 12. PMID: 18277380, doi:10.1038/msb.2008.5 Abstract: A striking and defining feature of circadian clocks is the small variation in period over a physiological range of temperatures. This is referred to as temperature compensation, although recent work has suggested that the variation observed is a specific, adaptive control of period. Moreover, given that many biological rate constants have a Q(10) of around 2, it is remarkable that such clocks remain rhythmic under significant temperature changes. We introduce a new mathematical model for the Neurospora crassa circadian network incorporating experimental work showing that temperature alters the balance of translation between a short and long form of the FREQUENCY (FRQ) protein. This is used to discuss period control and functionality for the Neurospora system. The model reproduces a broad range of key experimental data on temperature dependence and rhythmicity, both in wild-type and mutant strains. We present a simple mechanism utilising the presence of the FRQ isoforms (isoform switching) by which period control could have evolved, and argue that this regulatory structure may also increase the temperature range where the clock is robustly rhythmic. This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.For more information see the terms of use.To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Project description:Tseng2012 - Circadian clock of N.crassa A comprehensive model of the circardian clock of fungal Neurospora crassa , which encompasses existing knowledge of the biochemistry of Neurospora clock, is described by Tseng et al. (2012). The model is validated against a wide range of experimental phenotypes and has been used to investigate possible molecular explanations of temperature compensation. This model is described in the article: Comprehensive modelling of the Neurospora circadian clock and its temperature compensation. Tseng YY, Hunt SM, Heintzen C, Crosthwaite SK, Schwartz JM PLoS Comput. Biol. [2012 ; Volume: 8 (Issue: 3 )] Page info: e1002437 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. Figure 3 of the reference publication has been reproduced using Copasi 4.8 (Build 35). This model is hosted on BioModels Database and identified by: MODEL1212150000 . To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models . To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:The plant pathogenic fungus Verticillium dahliae has homologs of the clock genes [Cascant-Lopez et al., 2020], which are well described in Neurospora crassa [Diernfellner et al., 2020]. In N. crassa, frequency (Frq) and the Frq-interacting RNA helicase (Frh) interact and form the Frq-Frh complex [Cheng et al., 2005]. Formation of this complex was described to be still possible but weakened by a single amino acid exchange of arginine 806 of Frh to histidine (Frh^R806H) [Shi et al., 2010; Conrad et al., 2016]. We found that both FRQ and wild-type FRH were required for enhanced conidiation and the light-dependent repression of microsclerotia formation in V. dahliae, but were dispensable for disease induction in tomato plants. Strikingly, the FRH^R806H mutant strain grew similar to the FRQ deletion strain, although transcript and protein levels of Frq were not significantly affected by the FRH^R806H mutation when compared with the wild-type. Therefore, we hypothesized that V. dahliae Frq and Frh form the Frq-Frh complex to regulate V. dahliae development, and that this complex formation is abolished upon the amino acid exchange in the Frh. By the use of protein pull-downs, potential interactions of Frh-GFP or Frh^R806H-GFP with Frq were investigated. While we found evidence for a direct interaction of Frh-GFP and Frq, no proteins were significantly co-enriched with Frh^R806H-GFP. References: Cascant-Lopez, E.; Crosthwaite, S.K.; Johnson, L.J.; Harrison, R.J. No evidence that homologs of key circadian clock genes direct circadian programs of development or mRNA abundance in Verticillium dahliae. Front Microbiol 2020, 11, 1977, doi:10.3389/fmicb.2020.01977. Diernfellner, A.C.R.; Brunner, M. Phosphorylation timers in the Neurospora crassa circadian clock. J Mol Biol 2020, 432, 3449–3465, doi:10.1016/j.jmb.2020.04.004. Cheng, P.; He, Q.; He, Q.; Wang, L.; Liu, Y. Regulation of the Neurospora circadian clock by an RNA helicase. Genes Dev 2005, 19, 234–241, doi:10.1101/gad.1266805. Shi, M.; Collett, M.; Loros, J.J.; Dunlap, J.C. FRQ-interacting RNA helicase mediates negative and positive feedback in the Neurospora circadian clock. Genetics 2010, 184, 351–361, doi:10.1534/genetics.109.111393. Conrad, K.S.; Hurley, J.M.; Widom, J.; Ringelberg, C.S.; Loros, J.J.; Dunlap, J.C.; Crane, B.R. Structure of the frequency‐interacting RNA helicase: a protein interaction hub for the circadian clock. EMBO J 2016, 35, 1707–1719, doi:10.15252/embj.201694327.

Project description:Post-translational modifications (PTMs) on histones have been found to play diverse functions in regulating chromatin events and gene expression. The operation of circadian clocks heavily relies on finely tuned and timely expression of the proteins comprising core oscillators. However, most studies of PTMs’ effects on circadian clocks have been conducted using static systems in which circadian clocks are rendered arrhythmic due to the essential role of PTMs on gene expression. In the Neurospora circadian system, the White Collar Complex (WCC), a heterodimeric transcription factor formed from White Collar-1 (WC-1) and White Collar-2 (WC-2), serves the function of the BMAL1/CLOCK heterodimer in mammals, driving expression of circadian negative arm component(s), a principal one in Neurospora encoded by the gene frequency (frq). FRQ interacts with FRH (FRQ-interacting helicase) and CK-1 forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as brd-8, that encodes a conserved auxiliary subunit of the NuA4 histone acetylation complex. Loss of brd-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, BRD-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of brd-8, bye-1, histone hH2Az, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify new auxiliary elements of the fungal NuA4 complex having homology to mammalian components, which along with conventional NuA4 subunits, are required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.

Project description:Post-translational modifications (PTMs) on histones have been found to play diverse functions in regulating chromatin events and gene expression. The operation of circadian clocks heavily relies on finely tuned and timely expression of the proteins comprising core oscillators. However, most studies of PTMs' effects on circadian clocks have been conducted using static systems in which circadian clocks are rendered arrhythmic due to the essential role of PTMs on gene expression. In the Neurospora circadian system, the White Collar Complex (WCC), a heterodimeric transcription factor formed from White Collar-1 (WC-1) and White Collar-2 (WC-2), serves the function of the BMAL1/CLOCK heterodimer in mammals, driving expression of circadian negative arm component(s), a principal one in Neurospora encoded by the gene frequency (frq). FRQ interacts with FRH (FRQ-interacting helicase) and CK-1 forming a stable complex that represses its own expression by inhibiting WCC. In this study, a genetic screen identified a gene, designated as eaf-8, that encodes a novel conserved subunit of the NuA4 histone acetylation complex. Loss of eaf-8 reduces H4 acetylation and RNA polymerase (Pol) II occupancy at frq and other known circadian genes, and leads to a long circadian period, delayed phase, and defective overt circadian output at some temperatures. In addition to strongly associating with the NuA4 histone acetyltransferase complex, EAF-8 is also found complexed with the transcription elongation regulator BYE-1. Expression of eaf-8, bye-1, histone hH2Az, and several NuA4 subunits is controlled by the circadian clock, indicating that the molecular clock both regulates the basic chromatin status and is regulated by changes in chromatin. Taken together, our data identify a new type of the NuA4 complex including EAF-8 and BYE-1 which, along with conventional NuA4 subunits, is required for timely and dynamic frq expression and thereby a normal and persistent circadian rhythm.