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SEP3 and AG bind to regulatory elements in the AG locus [Kaufmann et al. , 2009], we assume in the
model that the AG/SEP (carpel) and the AG/SEP/PI/AP3 (stamen) protein complexes are functional in
this process.
Simulation parameters
The initial activation of the network, through the entities FD/FT, SOC1/AGL24 and a generic tran-
scription reaction acting on AP2 was given the speed 1 during the first 10 simulation cycles (a simulation
cycle corresponds to one Petri net time unit), and 0.01 thereafter as basal activity.
Transcription speeds were set so that the sum of transcription activation speeds from reactions simul-
taneously acting on an entity was equal or lower than 1, and each activation speed depended linearly
on the concentration of the activation factor under this limit. For every factor activating a given entity,
an independent transcription reaction was set, and the maximal speed of each reaction was chosen so
that the maximal combined speed of all the reactions that could be active simultaneously did not exceed
1. As an example, the AG mRNA is transcriptionally induced by LFY and, independently, also by the
complexes SEP/AG and SEP/AP3/PI/AG, so the maximal activation speed for each transcription reaction
was set to 0.33.
Translation speeds were set as the mRNA concentration divided by 5. Binding speeds were set as
the product of the concentration of the monomers divided by a constant, which was chosen to better
represent the biological implications of the network. In this case, the binding reactions were faster for
the petal and stamen complexes (the product of the monomer's concentration divided by 2) than for the
sepal and carpel complexes (the monomer's concentration divided by 5) following the supposition that
the heterodimers may have higher binding affinity than the homodimers [de Folter et al. , 2005]. The
degradation speeds were set as the concentration of an mRNA divided by 5, and the concentration of a
protein divided by 10, under the assumption that proteins are more stable than mRNAs [Matsuno et al. ,
2003]. The degradation speed of a protein complex was set as the concentration of the complex divided
by 15.
Exception from these rules were implemented to address the dependence of AP3 and PI on each other.
AP3 and PI stabilize each others expression and function as obligate heterodimers [Jack et al. , 1994; Hill
et al. , 1998; Tilly et al. , 1998]. To represent this dependence in the network, we assume that the single
monomer is extremely unstable and degrades fast, so we set the degradation speed of the protein to be 10
times the protein translation speed if the partner was absent. Reaction thresholds were set to 0.1, which
implies the requirement of a low protein concentration before the reaction becomes active.
The only exceptions to this rule were applied in the cases of the inhibition of AG by the petal complex
and the activation of AG by LFY, where the inhibition and activation thresholds were set to 1. In the first
case, the fact that low level presence of the petal complex in early stamen conditions would block the
stamen complex formation by inhibiting the transcription of AG . In the second case, LFY tends to be
expressed at a very low level, but still over the 0.1 threshold set in general. Under conditions where AG
is also expressed, the activity of low level LFY on AG would lead to an overproduction of this protein,
while the network structure suggests that AG depends on feedback from the protein complexes in which
it is present to keep its expression level. These threshold changes would have the biological implication
that the petal complex and LFY have a lower affinity to bind to the AG promoters than AP2 or the stamen
and carpel complexes. Further experimental data is necessary to elucidate the binding affinity differences
of these transcription factor complexes. Additionally, AG expression is also induced by other factors,
e.g. WUSCHEL [Lenhard et al. , 2001; Lohmann et al. , 2001], which were not considered in our simple
model.
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