Model Name: Arabidopsis_clock_P2011

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Version
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Version Comments

The SBML for this version uses the StepFunction (as in Adams et al. J. Biol Rhythms 2012) to represent the light-dark cycle. It has parameter name Lightstep, ID step1. Parameter name L, which is used in the model reactions, is assigned the value of Lightstep.

Note version 3 has a Copasi file attached.

 
Model Format SBML L2 V4
Description

This model is termed P2011 and derives from the article: The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar Mol. Syst. Biol. 2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. Link

Link to Supplementary Information, including equations. Minor errors in the published Supplementary Information are described in a file attached to version 1 of this model (the published SBML is correct).

 The model describes the circuit depicted in Fig. 1 of the paper (GIF attached). It updates the Pokhilko et al. 2010 model (termed P2010), PLM_6, by including:

  1. the Evening Complex genes (ELF4, ELF3, LUX),
  2. light-regulated degradation of ELF3 by COP1,
  3. TOC1 as a repressor rather than an activator of LHY/CCA1.

These changes allowed the removal of hypothetical components TOC1mod (or X) and Y from the earlier models. They also reveal that the central loop of the model is a triple-repressor ring oscillator, or 'repressilator' (illustrated in Fig. 8, GIF attached).

SBML curation notes (please see Comments for each version): Compared to the model version submitted to the Biomodels database, version 1 here slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. A MATLAB version is attached to version 1. In version 2, the rule is used with a generic SBML StepFunction (Adams et al. J. Biol. Rhythms Aug 2012) to describe the light-dark cycle more flexibly. Versions 1 and 2 have multiple sinks and sources created by CellDesigner. These are removed in versions 3 & 4. Version 3 has the published lightfunction, and an equivalent COPASI file attached. Version 4 has the StepFunction.

 
Contact/Model Admin Andrew Millar, University of Edinburgh, andrew.millar@ed.ac.uk
Submitted By Andrew Millar, University of Edinburgh, andrew.millar@ed.ac.uk
Submission Date 2012-03-07 12:15:12.0
Images
thumbnail Fig. 1, outline of P2011 model, with P2010 inset
thumbnail Fig. 8, cartoon illustrating repressilator structure
Supplementary Data Files
ODE file for Matlab version of P2011 clock model
Matlab version of P2011 clock model
Model Files original file, simplified file (use simplified if your software cannot read the file, e.g. Sloppy Cell)
Journal Mol. Syst. Biol. 8: 574. 
Title The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. 
Year 2012 
Authors Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar 
Abstract Circadian clocks synchronise biological processes with the day/night cycle, using molecular mechanisms that include interlocked, transcriptional feedback loops. Recent experiments identified the evening complex (EC) as a repressor that can be essential for gene expression rhythms in plants. Integrating the EC components in this role significantly alters our mechanistic, mathematical model of the clock gene circuit. Negative autoregulation of the EC genes constitutes the clock's evening loop, replacing the hypothetical component Y. The EC explains our earlier conjecture that the morning gene PSEUDO-RESPONSE REGULATOR 9 was repressed by an evening gene, previously identified with TIMING OF CAB EXPRESSION1 (TOC1). Our computational analysis suggests that TOC1 is a repressor of the morning genes LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK ASSOCIATED1 rather than an activator as first conceived. This removes the necessity for the unknown component X (or TOC1mod) from previous clock models. As well as matching timeseries and phase-response data, the model provides a new conceptual framework for the plant clock that includes a three-component repressilator circuit in its complex structure. 
URL http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html 
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1. Comment by amillar2 on 2012-06-01 17:29:46.0

Version 2 of the model includes the StepFunction. Note that we have not yet removed the original light function parameter names, they are now non-functional.