Figure 1.
The F2014 model of the Arabidopsis circadian clock.
Components of the clock are laid out according to approximate time of peak mRNA expression, clockwise with zeitgeber time 0 (lights on) at the bottom. Yellow and grey boxes indicate proteins that are active primarily during the day and night, respectively. Solid lines indicate transcriptional regulation and dashed lines indicate protein–protein interactions, with arrows for activation and bars for repression or degradation. Additions to the model relative to P2012 are shown in blue. The green line indicates a hypothetical interaction, and the light grey line indicates an interaction that the model predicts to be extremely weak. The light blue boxes show three main modules of the clock, and interactions between them are shown with thick black lines. EC is the evening complex between ELF3, ELF4 and LUX or NOX, and the dark grey line indicates the ELF3-ELF4 complex. Lightning and yellow circles symbolize light input at the transcriptional and post-transcriptional level, respectively. For an alternative version comparing F2014 with P2012 [6] (published 2013), see Figure S1.
Figure 2.
The evening complex and its components.
Concentration levels of a selection of model components relevant to EC, in the transition from LD 12:12 (light/dark cycles) to LL (constant light), comparing our ensemble of models (eight parameter sets, black lines), to the previous models P2011 (dashed red line) and P2012 (dotted blue line). (A) ELF3 mRNA in wild type (wt), compared with a typical experiment (green triangles, data from [51]). (B) ELF3 protein in the nucleus, not counting complexes. (C) The ELF3-ELF4 protein complex. (D) The resulting evening complex. Each curve was normalized to a peak level of 1. Grey background signifies the night of the last day of LD before the transition to LL at ZT 24.
Figure 3.
NOX and its interaction with CCA1.
Comparison between the F2014 model (eight parameter sets, black lines) and experimental data (green triangles [31], blue circles [30], red squares [52] and purple diamonds [53]), and the earlier models P2011 (dashed red lines) and P2012 (dotted blue lines), where applicable, in the transition from LD to LL. (A) NOX mRNA in wt. (B) LUX mRNA in wt. (C–F) CCA1 mRNA in (C) wt, (D) nox mutant (boa-1), (E) lux mutant (pcl1-1), and (F) NOX-ox. The peak mRNA levels for the models were normalized to 1 in wt, and the same normalization was kept for the mutants. Experimental data were scaled to match the model in panel C, and the same normalization was used in panels D–F. Note the different y scales.
Figure 4.
Expression and regulation of the PRR genes.
(A–C) The mRNA levels of PRR9 (solid red), PRR7 (long dashed green), PRR5 (short dashed blue) and TOC1 (dotted black) in the transition from LD to LL. (A) The F2014 model with eight different parameter sets. (B) Experimental data: PRR9 [35], [36], [54], PRR7 [35], [54], [55], PRR5 [29], [55], [56] and TOC1 [53], [57], [58]. (C) The P2012 and P2011 models (thick and thin lines, respectively). (D) Total PRR5 protein level in prr9;prr7 in LD in F2014 (solid black), P2011 (dashed red), P2012 (dotted blue) and experimental data (green triangles [54]). (E) The predicted repression of PRR transcription by CCA1 and LHY, as a multiplicative factor, with colours as in (A–C). (F) PRR9 mRNA in cca1-11;lhy-21 in LD, normalized to the corresponding wt curves in (A–C); colours as in (D) but data from [11]. The peak levels in (A), (C) and (D) were normalized to 1, whereas the levels in (B) were adjusted manually.
Figure 5.
The effects of RVE8 in the model.
(A–C) Expression levels in the transition from LD to LL, comparing the model (eight parameter sets, solid black lines) with experimental data (green triangles [29], red squares [59], blue circles [28] and purple diamonds [60]). (A) RVE8 mRNA in wt, (B) LHY in wt, and (C) LHY in rve4;rve6;rve8. (D–F) The effect of RVE8 on each of its target genes, as a time-dependent multiplicative factor, in the eight parameter sets. (D) PRR9 (solid red) and PRR5 (dotted blue), (E) GI (solid green) and TOC1 (dotted black), and (F) LUX (solid purple) and ELF4 (dotted light blue).
Table 1.
The number of parameters and variables in different Arabidopsis clock models.