BioModels Database logo

BioModels Database

spacer

BIOMD0000000214 - Akman2008_Circadian_Clock_Model2

 

 |   |   |  Send feedback
Reference Publication
Publication ID: 18277380
Akman OE, Locke JC, Tang S, Carré I, Millar AJ, Rand DA.
Isoform switching facilitates period control in the Neurospora crassa circadian clock.
Mol. Syst. Biol. 2008; 4: 164
Centre for Systems Biology at Edinburgh, The University of Edinburgh, Edinburgh, UK [corrected]  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission ID: MODEL8306015773
Submission Date: 04 Jun 2009 16:03:50 UTC
Last Modification Date: 28 May 2014 01:57:42 UTC
Creation Date: 03 Dec 2008 12:40:28 UTC
Encoders:  Lukas Endler
   Vijayalakshmi Chelliah
   Ozgur Akman
set #1
bqmodel:isDerivedFrom BioModels Database Leloup1999_CircadianRhythms_Neurospora
set #2
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
Gene Ontology circadian rhythm
set #3
bqbiol:hasTaxon Taxonomy Neurospora crassa
Notes

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.

Model
Publication ID: 18277380 Submission Date: 04 Jun 2009 16:03:50 UTC Last Modification Date: 28 May 2014 01:57:42 UTC Creation Date: 03 Dec 2008 12:40:28 UTC
Mathematical expressions
Reactions
MFtrn MFdeg E1Ftrl E1Fdeg
E2Ftrl E2Fdeg PFtrl PFdeg
MWtrn MWdeg E1Wtrl E1Wdeg
E2Wtrl E2Wdeg PWtrl PWdeg
PWtrs PWLdeg E1Fptrl E1Fpdeg
E2Fptrl E2Fpdeg PFptrl PFpdeg
Rules
Assignment Rule (variable: tot s-Frq) Assignment Rule (variable: tot l-Frq) Assignment Rule (variable: tot Frq) Assignment Rule (variable: tot WC-1)
Physical entities
Compartments Species
cytosol s-Frq_1 l-Frq_1 WC-1_1
s-Frq_2 l-Frq_2 WC-1_2
     
nucleus Frq mRNA WC-1 mRNA s-Frq
l-Frq WC-1 WC-1*
tot s-Frq tot l-Frq tot Frq
tot WC-1    
Global parameters
a1 a2 a3 a4
a5 a6 a7 b1
b2 b3 b4 b5
b7 b8 b9 b10
b6 d1 d2 d3
d4 d5 f1 f2
gam1 gam2 r1 r2
n m k a3p
d2p f1p gam1p amp
dawn dusk    
Reactions (24)
 
 MFtrn  → [Frq mRNA];   {s-Frq} , {l-Frq} , {WC-1} , {WC-1*}
 
 MFdeg [Frq mRNA] → ;  
 
 E1Ftrl  → [s-Frq_1];   {Frq mRNA}
 
 E1Fdeg [s-Frq_1] → ;  
 
 E2Ftrl [s-Frq_1] → [s-Frq_2];  
 
 E2Fdeg [s-Frq_2] → ;  
 
 PFtrl [s-Frq_2] → [s-Frq];  
 
 PFdeg [s-Frq] → ;  
 
 MWtrn  → [WC-1 mRNA];   {WC-1*}
 
 MWdeg [WC-1 mRNA] → ;  
 
 E1Wtrl  → [WC-1_1];   {WC-1 mRNA} , {s-Frq} , {l-Frq}
 
 E1Wdeg [WC-1_1] → ;  
 
 E2Wtrl [WC-1_1] → [WC-1_2];  
 
 E2Wdeg [WC-1_2] → ;  
 
 PWtrl [WC-1_2] → [WC-1];  
 
 PWdeg [WC-1] → ;  
 
 PWtrs [WC-1] ↔ [WC-1*];  
 
 PWLdeg [WC-1*] → ;  
 
 E1Fptrl  → [l-Frq_1];   {Frq mRNA}
 
 E1Fpdeg [l-Frq_1] → ;  
 
 E2Fptrl [l-Frq_1] → [l-Frq_2];  
 
 E2Fpdeg [l-Frq_2] → ;  
 
 PFptrl [l-Frq_2] → [l-Frq];  
 
 PFpdeg [l-Frq] → ;  
 
Rules (4)
 
 Assignment Rule (name: sFrq_tot) tot s-Frq = PF+E2F+E1F
 
 Assignment Rule (name: lFrq_tot) tot l-Frq = PFp+E2Fp+E1Fp
 
 Assignment Rule (name: Frq_tot) tot Frq = sFrq_tot+lFrq_tot
 
 Assignment Rule (name: WC1_tot) tot WC-1 = PW+PWL+E1W+E2W
 
 cytosol Spatial dimensions: 3.0  Compartment size: 1.0
 
 s-Frq_1
Compartment: cytosol
Initial concentration: 0.43076
 
 l-Frq_1
Compartment: cytosol
Initial concentration: 0.45583
 
 WC-1_1
Compartment: cytosol
Initial concentration: 5.84748
 
 s-Frq_2
Compartment: cytosol
Initial concentration: 0.10647
 
 l-Frq_2
Compartment: cytosol
Initial concentration: 0.09872
 
 WC-1_2
Compartment: cytosol
Initial concentration: 5.70265
 
 nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 Frq mRNA
Compartment: nucleus
Initial concentration: 0.6935
 
 WC-1 mRNA
Compartment: nucleus
Initial concentration: 1.2689
 
 s-Frq
Compartment: nucleus
Initial concentration: 0.06565
 
 l-Frq
Compartment: nucleus
Initial concentration: 0.07719
 
 WC-1
Compartment: nucleus
Initial concentration: 26.4393
 
 WC-1*
Compartment: nucleus
Initial concentration: 0.0
 
  tot s-Frq
Compartment: nucleus
 
  tot l-Frq
Compartment: nucleus
 
  tot Frq
Compartment: nucleus
 
  tot WC-1
Compartment: nucleus
 
Global Parameters (38)
 
   a1
Value: 24.9736
Constant
 
   a2
Value: 3.59797
Constant
 
   a3
Value: 0.2834
Constant
 
   a4
Value: 0.46227
Constant
 
   a5
Value: 0.02917
Constant
 
   a6
Value: 0.20695
Constant
 
   a7
Value: 3.02856
Constant
 
   b1
Value: 0.00209
Constant
 
   b2
Value: 2.13476
Constant
 
   b3
Value: 0.08039
Constant
 
   b4
Value: 0.45859
Constant
 
   b5
Value: 0.13056
Constant
 
   b7
Value: 2.96739
Constant
 
   b8
Value: 0.11167
Constant
 
   b9
Value: 81.10381
Constant
 
   b10
Value: 93.03664
Constant
 
   b6
Constant
 
   d1
Value: 1.43549
Constant
 
   d2
Value: 0.21251
Constant
 
   d3
Value: 0.50309
Constant
 
   d4
Value: 3.36641
Constant
 
   d5
Value: 0.41085
Constant
 
   f1
Value: 0.09292
Constant
 
   f2
Value: 0.14979
Constant
 
   gam1
Value: 0.34603
Constant
 
   gam2
Value: 2.8E-4
Constant
 
   r1
Value: 2.71574
Constant
 
   r2
Value: 35.40005
Constant
 
   n
Value: 1.02419
Constant
 
   m
Value: 1.34979
Constant
 
   k
Value: 2.18234
Constant
 
   a3p
Value: 0.34578
Constant
 
   d2p
Value: 0.18191
Constant
 
   f1p
Value: 0.09588
Constant
 
   gam1p
Value: 0.40119
Constant
 
   amp
Constant
 
   dawn
Value: 12.0
Constant
 
   dusk
Value: 24.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000214

Curator's comment: (updated: 04 Jun 2009 17:03:29 BST)

reproduction of figure 6 from the supplementary information. the simulation was performed using Copasi

spacer
spacer