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Mathematical model of the Arabidopsis circadian clock: Pokhilko 2011 model

Research output: Other contribution

Original languageEnglish
Media of outputSBML model
Publication statusPublished - 2012


[from the record in PlaSMo] 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, published 6 March 2012. Link

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:

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).

Compared to the model version submitted to the Biomodels database, this version slightly alters the names of some variables and uses an SBML AssignmentRule for the light input. This will facilitate the use of a generic SBML StepFunction to better describe the light-dark cycle, in a subsequent version of this model.

    Research areas

  • Biological Clocks, Circadian Rhythms, mathematical modeling, MODEL SIMULATION, Systems Biology

ID: 2022241