Arabidopsis_clock_P2011 - PLM_64, version 2

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.

Related Publications
Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar (2012). The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops.. Mol. Syst. Biol. 8: 574.. Retrieved from: http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html

Comments


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.


2012-06-01 17:29:46 3 amillar2 andrew.millar@ed.ac.uk

Originally submitted to PLaSMo on 2012-03-07 12:15:12

SEEK ID: https://fairdomhub.org/assays/839

Modelling Analysis

BioData SynthSys

Projects: Millar group, PlaSMo model repository

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis_clock_P2011 - PLM_64

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

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Andrew Millar
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Created: 10th Jan 2019 at 17:40

Last updated: 22nd Jan 2019 at 18:17

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