Arabidopsis_clock_P2011 - PLM_64, version 3

Overview
Related items

This model is termed P2011 and derives from the article: <strong>The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops</strong><strong>. </strong>Alexandra Pokhilko, Aurora Piñas Fernández, Kieron D Edwards, Megan M Southern, Karen J Halliday & Andrew J Millar <em>Mol. Syst. Biol. </em>2012; 8: 574, submitted 9 Aug 2011 and published 6 March 2012. <a href="http://www.nature.com/msb/journal/v8/n1/synopsis/msb20126.html">Link</a>	Link to <a href="http://www.nature.com/msb/journal/v8/n1/extref/msb20126-s1.pdf">Supplementary Information</a>, 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), <a href="http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_6">PLM_6</a>, by including:<ol>

the Evening Complex genes (ELF4, ELF3, LUX),

light-regulated degradation of ELF3 by COP1,

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

Version Comments

The SBML for this version uses the lightfunction (as in Mol Syst Biol 2012 paper) to represent the light-dark cycle. It is assigned to parameter name L, which is used in the model reactions.

However, the internal parameters of lightfunction have default Copasi ID's, parameter_1 to parameter_6, with names that match the publication (photperiod, etc.). A COPASI file for this model is also attached.

This model is equivalent to the published version, referred to as P2011.1.1 in our later paper (Flis et al. RSOB 2015).

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

SEEK ID: https://fairdomhub.org/assays/840

Class: Modelling Analysis

Submitter: BioData SynthSys

Projects: Millar group, PlaSMo model repository

Investigation: Millar, Andrew (ex-PlaSMo models)

Study: Arabidopsis_clock_P2011 - PLM_64

Assay position:

Biological problem addressed: Gene Regulatory Network

Organisms: Arabidopsis thaliana

Models: