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identity transcription factors leads to the formation of protein dimers (SEP/AP1, AP3/PI, SEP/AG) and
higher-order complexes (SEP/AP1/AP3/PI and SEP/AP3/PI/AG).
Even though some of the factors that control spatial expression domains of organ identity genes in
flower development are already known (e.g.
SUP
,
UFO
,
miR172
), the upstream regulation of these spatial
control genes remains to be elucidated. In this network model, the simulation started from a set of 4
different initial conditions that replicate the known activities of these spatial regulators. These initial
conditions depend on the value of the 3 spatial regulators UFO, SUP and miR172.
The concentration values for the entities of the spatial regulators SUP and miR172 were set to 0 or 1
as on/off states. The translation speed of UFO was chosen to maintain the biological congruence of the
network, at 0.5 units per simulation cycle in active state, and 0 when inactive. According to the model
network, high concentrations of UFO would sequester the protein LFY and alter the expression patterns
of
AP1
/
CAL
and
SEP
, which are regulated by LFY alone; thus the chosen speed allows the presence of
free LFY protein.
The initial conditions sets were then chosen as follows:
-
SUP
on,
miR172
off and
UFO
off leading to sepal formation: The presence of AP2 inhibits expression
of
AG
. Since
UFO
is off and
SUP
is on, there is no AP3/PI production, leading to the expression of
SEP/AP1 as steady-state TF complex.
-
SUP
off,
miR172
off and
UFO
on leading to petal formation: The expression of UFO leads to the
formation of the dimer UFO/SEP which activates the expression of
AP3
/
PI
. The presence of AP2
inhibits expression of
AG
and allows expression of
AP1
, leading to the formation of the steady-state
TF complex SEP/AP1/AP3/PI.
-
SUP
off,
miR172
on and
UFO
on leading to stamen formation: inhibition of
AP2
by miR172 allows
AG
to be expressed, and the presence of UFO activates the expression of
AP3
/
PI
. AP1 is transiently
expressed before the TF complexes that inhibit it are formed, but once AG complexes are formed,
AP1
is inhibited, leading to the formation of the steady-state TF SEP/AP3/PI/AG.
-
SUP
on,
miR172
on and
UFO
off leading to carpel formation: SUP inhibits
AP3
/
PI
, and the inhibition
of
AP2
by miR172 allows expression of
AG
, leading to SEP/AG formation. This factor also inhibits
AP1
when formed but allows a transient expression in early simulation time.
The final network is provided as a file in Cell Illustrator's CSML format, and can be inspect-
ed and simulated by using the free Cell Illustrator Player program launched from a web browser
Experimental support for interactions described in the network
Floral meristem identity genes. The closely related MADS-box genes
APETALA1
and
CAULIFLOW-
ER
(
AP1
/
CAL
) as well as the NonMADS transcription factor
LEAFY
(
LFY
) control the initial specification
of flowers in response to different floral induction pathways [Huala and Sussex, 1992; Mandel
et al.
,
1992; Weigel
et al.
, 1992]. All three genes are expressed at the earliest stages of floral meristem devel-
opment and LFY and AP1 are known to positively upregulate each others' expression [Liljegren
et al.
,
1999].
AP1
and
CAL
are two closely related paralogous MADS-box genes with highly redundant func-
tion [Kempin
et al.
, 1995], and are therefore treated as one functional molecule in our network. AP1 has
a second role at later stages of flower development in the specification of sepal and petal identity [Mandel
et al.
, 1992]. AP1 and CAL form dimers with SEPALLATA (SEP) MADS-domain proteins [Pelaz
et
al.
, 2001; Castillejo
et al.
, 2005] and interact in a higher-order complex with APETALA3 (AP3) and
PISTILLATA (PI) [Honma and Goto, 2001]. According to the 'quartet model' of flower development, the
