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BIOMD0000000631 - DeCaluwe2016 - Circadian Clock

 

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Reference Publication
Publication ID: 26904049
De Caluwé J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D.
A Compact Model for the Complex Plant Circadian Clock.
Front Plant Sci 2016; 7: 74
Unité de Chronobiologie Théorique, Faculté des Sciences, Université Libre de Bruxelles Brussels, Belgium.  [more]
Model
Original Model: BIOMD0000000631.origin
Submitter: Vijayalakshmi Chelliah
Submission ID: MODEL1601130000
Submission Date: 13 Jan 2016 14:17:51 UTC
Last Modification Date: 11 Apr 2017 13:14:51 UTC
Creation Date: 29 Mar 2017 19:16:23 UTC
Encoders:  Ryan Gutenkunst
   Varun Kothamachu
   David Jones
   Rachel Victor
   Nick Helle
   Kathleen Lasick
   Alyssa Fortier
set #1
bqbiol:hasTaxon Taxonomy Arabidopsis thaliana
bqbiol:isVersionOf Gene Ontology regulation of circadian rhythm
Gene Ontology entrainment of circadian clock by photoperiod
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
Notes
DeCaluwé2016 - Circadian Clock

This model is described in the article:

De Caluwé J, Xiao Q, Hermans C, Verbruggen N, Leloup JC, Gonze D.
Front Plant Sci 2016; 7: 74

Abstract:

The circadian clock is an endogenous timekeeper that allows organisms to anticipate and adapt to the daily variations of their environment. The plant clock is an intricate network of interlocked feedback loops, in which transcription factors regulate each other to generate oscillations with expression peaks at specific times of the day. Over the last decade, mathematical modeling approaches have been used to understand the inner workings of the clock in the model plant Arabidopsis thaliana. Those efforts have produced a number of models of ever increasing complexity. Here, we present an alternative model that combines a low number of equations and parameters, similar to the very earliest models, with the complex network structure found in more recent ones. This simple model describes the temporal evolution of the abundance of eight clock gene mRNA/protein and captures key features of the clock on a qualitative level, namely the entrained and free-running behaviors of the wild type clock, as well as the defects found in knockout mutants (such as altered free-running periods, lack of entrainment, or changes in the expression of other clock genes). Additionally, our model produces complex responses to various light cues, such as extreme photoperiods and non-24 h environmental cycles, and can describe the control of hypocotyl growth by the clock. Our model constitutes a useful tool to probe dynamical properties of the core clock as well as clock-dependent processes.

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.

Model
Publication ID: 26904049 Submission Date: 13 Jan 2016 14:17:51 UTC Last Modification Date: 11 Apr 2017 13:14:51 UTC Creation Date: 29 Mar 2017 19:16:23 UTC
Mathematical expressions
Reactions
CL_transcription CL_light_transcription CLm_light_degradation CLm_dark_degradation
CL_translation CL_light_translation CLp_degradation P97_light_transcription
P97_transcription P97_CL_transcription P97m_degradation P97_translation
P97_dark_degradation P97_light_degradation P51_transcription P51m_degradation
P51_translation P51_dark_degradation P51_light_degradation EL_light_transcription
ELm_degradation EL_translation EL_dark_degradation EL_light_degradation
P_dark_accumulation P_light_degradation PIF_transcription PIFm_degradation
PIF_translation PIF_dark_degradation PIF_light_degradation basal_growth
PIF_induced_growth      
Physical entities
Compartments Species
cell CCA1/LHY mRNA CCA1/LHY protein PRR9/PRR7 mRNA
PRR9/PRR7 protein PRR5/TOC1 mRNA PRR5/TOC1 protein
ELF4/LUX mRNA ELF4/LUX protein PIF4/PIF5 mRNA
PIF4/PIF5 protein Hypocotyl length P
Global parameters
v1 v1L v2A v2B
v3 v4 k1L v2L
k1D k2 k3 k4
p1 p1L p2 p3
p4 d1 d2D d2L
d3D d3L d4D d4L
K1 K2 K3 K4
K5 K6 K7 K8
K9 K10 v5 k5
p5 d5L d5D g1
g2 K11 K12 Photoperiod
Cycle length Light Dark  
Reactions (33)
 
 CL_transcription  ↔ [CCA1/LHY mRNA];   {PRR5/TOC1 protein} , {PRR9/PRR7 protein}
 
 CL_light_transcription  ↔ [CCA1/LHY mRNA];   {PRR5/TOC1 protein} , {PRR9/PRR7 protein} , {P}
 
 CLm_light_degradation [CCA1/LHY mRNA] ↔ ;  
 
 CLm_dark_degradation [CCA1/LHY mRNA] ↔ ;  
 
 CL_translation  ↔ [CCA1/LHY protein];   {CCA1/LHY mRNA}
 
 CL_light_translation  ↔ [CCA1/LHY protein];   {CCA1/LHY mRNA}
 
 CLp_degradation [CCA1/LHY protein] ↔ ;  
 
 P97_light_transcription  ↔ [PRR9/PRR7 mRNA];   {PRR5/TOC1 protein} , {ELF4/LUX protein} , {P}
 
 P97_transcription  ↔ [PRR9/PRR7 mRNA];   {PRR5/TOC1 protein} , {ELF4/LUX protein}
 
 P97_CL_transcription  ↔ [PRR9/PRR7 mRNA];   {PRR5/TOC1 protein} , {CCA1/LHY protein} , {ELF4/LUX protein}
 
 P97m_degradation [PRR9/PRR7 mRNA] ↔ ;  
 
 P97_translation  ↔ [PRR9/PRR7 protein];   {PRR9/PRR7 mRNA}
 
 P97_dark_degradation [PRR9/PRR7 protein] ↔ ;  
 
 P97_light_degradation [PRR9/PRR7 protein] ↔ ;  
 
 P51_transcription  ↔ [PRR5/TOC1 mRNA];   {PRR5/TOC1 protein} , {CCA1/LHY protein}
 
 P51m_degradation [PRR5/TOC1 mRNA] ↔ ;  
 
 P51_translation  ↔ [PRR5/TOC1 protein];   {PRR5/TOC1 mRNA}
 
 P51_dark_degradation [PRR5/TOC1 protein] ↔ ;  
 
 P51_light_degradation [PRR5/TOC1 protein] ↔ ;  
 
 EL_light_transcription  ↔ [ELF4/LUX mRNA];   {PRR5/TOC1 protein} , {CCA1/LHY protein} , {ELF4/LUX protein}
 
 ELm_degradation [ELF4/LUX mRNA] ↔ ;  
 
 EL_translation  ↔ [ELF4/LUX protein];   {ELF4/LUX mRNA}
 
 EL_dark_degradation [ELF4/LUX protein] ↔ ;  
 
 EL_light_degradation [ELF4/LUX protein] ↔ ;  
 
 P_dark_accumulation  ↔ [P];  
 
 P_light_degradation [P] ↔ ;  
 
 PIF_transcription  ↔ [PIF4/PIF5 mRNA];   {ELF4/LUX protein}
 
 PIFm_degradation [PIF4/PIF5 mRNA] ↔ ;  
 
 PIF_translation  ↔ [PIF4/PIF5 protein];   {PIF4/PIF5 mRNA}
 
 PIF_dark_degradation [PIF4/PIF5 protein] ↔ ;  
 
 PIF_light_degradation [PIF4/PIF5 protein] ↔ ;  
 
 basal_growth  ↔ [Hypocotyl length];  
 
 PIF_induced_growth  ↔ [Hypocotyl length];   {PIF4/PIF5 protein}
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 CCA1/LHY mRNA
Compartment: cell
Initial concentration: 1.0
 
 CCA1/LHY protein
Compartment: cell
Initial concentration: 1.0
 
 PRR9/PRR7 mRNA
Compartment: cell
Initial concentration: 1.0
 
 PRR9/PRR7 protein
Compartment: cell
Initial concentration: 1.0
 
 PRR5/TOC1 mRNA
Compartment: cell
Initial concentration: 1.0
 
 PRR5/TOC1 protein
Compartment: cell
Initial concentration: 1.0
 
 ELF4/LUX mRNA
Compartment: cell
Initial concentration: 1.0
 
 ELF4/LUX protein
Compartment: cell
Initial concentration: 1.0
 
 PIF4/PIF5 mRNA
Compartment: cell
Initial concentration: 1.0
 
 PIF4/PIF5 protein
Compartment: cell
Initial concentration: 1.0
 
 Hypocotyl length
Compartment: cell
Initial concentration: 1.0
 
 P
Compartment: cell
Initial concentration: 1.0
 
Global Parameters (47)
 
   v1
Value: 4.58
Constant
 
   v1L
Value: 3.0
Constant
 
   v2A
Value: 1.27
Constant
 
   v2B
Value: 1.48
Constant
 
   v3
Value: 1.0
Constant
 
   v4
Value: 1.47
Constant
 
   k1L
Value: 0.53
Constant
 
   v2L
Value: 5.0
Constant
 
   k1D
Value: 0.21
Constant
 
   k2
Value: 0.35
Constant
 
   k3
Value: 0.56
Constant
 
   k4
Value: 0.57
Constant
 
   p1
Value: 0.76
Constant
 
   p1L
Value: 0.42
Constant
 
   p2
Value: 1.01
Constant
 
   p3
Value: 0.64
Constant
 
   p4
Value: 1.01
Constant
 
   d1
Value: 0.68
Constant
 
   d2D
Value: 0.5
Constant
 
   d2L
Value: 0.29
Constant
 
   d3D
Value: 0.48
Constant
 
   d3L
Value: 0.78
Constant
 
   d4D
Value: 1.21
Constant
 
   d4L
Value: 0.38
Constant
 
   K1
Value: 0.16
Constant
 
   K2
Value: 1.18
Constant
 
   K3
Value: 0.24
Constant
 
   K4
Value: 0.23
Constant
 
   K5
Value: 0.3
Constant
 
   K6
Value: 0.46
Constant
 
   K7
Value: 2.0
Constant
 
   K8
Value: 0.36
Constant
 
   K9
Value: 1.9
Constant
 
   K10
Value: 1.9
Constant
 
   v5
Value: 0.1
Constant
 
   k5
Value: 0.14
Constant
 
   p5
Value: 0.62
Constant
 
   d5L
Value: 4.0
Constant
 
   d5D
Value: 0.52
Constant
 
   g1
Value: 0.01
Constant
 
   g2
Value: 0.12
Constant
 
   K11
Value: 0.21
Constant
 
   K12
Value: 0.56
Constant
 
 Photoperiod
Value: 12.0
Constant
 
 Cycle length
Value: 24.0
Constant
 
 Light
Value: 1.0
 
 Dark  
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000631

Curator's comment: (updated: 29 Mar 2017 17:03:46 BST)

This model was validated by reproducing figure 2 in the article using SloppyCell and COPASI (4.16 (Build 104)).

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