Arabidopsis_clock_P2011 - PLM_64, version 4

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 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.

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

SEEK ID: https://fairdomhub.org/assays/841

Class: Modelling analysis

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: No organisms

Models:

Data: