Troein Ostreococcus clock 1-loop - PLM_7, version 1

This is a model of the circadian clock of Ostreococcus tauri, with a single negative feedback loop between TOC1 and CCA1 (a.k.a. LHY), and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011). The model has been tested in Copasi, where it reproduces the behaviour of the original (which consisted of equations loaded from a text file by a more or less custom C++ program).

Comments


Not formulated to easily allow addition of the ISSF to replace the present light function.


2013-02-27 12:34:55 3 amillar2 andrew.millar@ed.ac.uk

Version Comments


This is a model of the circadian clock of Ostreococcus tauri, with a negative feedback loop between TOC1 and CCA1 (a.k.a. LHY) and multiple light inputs. It was used and described in Troein et al., Plant Journal (2011).
The model incorporates luciferase reporters, and in this SBML model the four different versions of the model for transcriptional and translational reporter lines (pTOC1::LUC, pCCA1::LUC, TOC1-LUC and CCA1-LUC) are all accessible by setting one of the rep_X parameters to 1 and the others to 0. You can also set all four to 0 to only simulate the non-reporter core of the system.
Input to the system should be provided by modifying the "light" function. The functions "ox_cca1" and "ox_toc1" can be altered to add overexpression of CCA1 and TOC1. Setting either to x gives additional, constitutive transcription at x times the transcription rate that the native gene has when the Shea-Ackers quotient equals 1. The functions "copies_toc1" and "copies_cca1" are normally 1 but can be lowered to simulate knockdown experiments. The functions "transcription", "translation" and "proteasome" can be used to modify the overall rate of transcription, translation and protein degradation.
The parameters were fitted specifically to data from transgenic reporter lines TOC8, pTOC3, LHY7 and pLHY7 (Corellou et al., Plant Cell 2009). Parameters that begin with "effcopies" describe the effective number of copies of CCA1 or TOC1 in the respective translational fusion lines, with anything above 1 due to the fusion proteins.
For the model fitting, the initial values were fitted to the data in the various time courses. The initial values given here correspond to the limit cycle of the system in LD 12:12. The system converges to the limit cycle in just a few days under most light conditions, so these initial values are biologically meaningful.
The species cca1luc_c and cca1luc_n have been merged into cca1luc (which corresponds to the observable signal), because Copasi refused to run the system otherwise. For TOC1-LUC, the predicted signal is the sum of toc1luc_1 and toc1luc_2.




Originally submitted to PLaSMo on 2010-05-04 11:27:33

SEEK ID: https://fairdomhub.org/assays/912

Modelling Analysis

BioData SynthSys

Projects: PlaSMo model repository

Investigation: Troein, Carl

Study: Troein Ostreococcus clock 1-loop - PLM_7

Biological problem addressed: Gene Regulatory Network

Organisms: No organisms

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Carl Troein, Andrew Millar
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Created: 10th Jan 2019 at 17:42

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