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A Circadian Clock-Regulated Toggle Switch Explains AtGRP7 and AtGRP8 Oscillations in Arabidopsis thaliana

Figure 3

The model properly fits experimental data.

A) Simulated AtGRP7 and B) AtGRP8 mRNA oscillations under 12h∶12h LD conditions (blue curves) are plotted together with the corresponding “COL_LDHH” experimental data set from the DIURNAL database (green curves with markers indicating data points), which uses Columbia wild type plants investigated under 12h∶12h LD entrainment condition with a constant temperature of . The DIURNAL database collects circadian microarray time series data based on Affymetrix chips and was normalized using gcRMA [25]. C) Simulated AtGRP7 mRNA and D) protein oscillations under LL conditions, after entrainment under 8h∶16h LD conditions, are plotted together with the corresponding RNA and protein gel blot data taken from [22]. In [22], this gel blot data was published relative to the minimal level, which was defined as 1. Note that the time axis of the experimental data was adjusted by +34 hours. This takes into account a shortcoming of the core oscillator model adopted from [11], namely that the phase of the simulated LHY/CCA1 mRNA oscillations under LL conditions in this core oscillator model only agrees with the corresponding data in the DIURNAL database (data sets “LL12_LDHH” and “LL23_LDHH” in [25]), if the time axis of those experimental data is adjusted by approximately ten hours. Since the samples in the experiments [74], [75] underlying these data sets were collected on days two and three after transferring the plants to LL conditions, we also did not take into account the first day in LL, altogether thus amounting to a total time-adjustment of +34h. Overall, the agreement between the simulated and experimental phases, periods, and waveforms is very good.

doi: https://doi.org/10.1371/journal.pcbi.1002986.g003