The signaling circuit

The signaling circuit 3 described in the Circuit Section has been modeled using Matlab Simbiology desktop. The following diagram shows the different parts of the model we have simulated:

For the level of detail considered, the main parts simulated are the following (the number correspond to the equations listed in the table in the next section):

Generation of L_aspartate induced by AAL
Diffusion of L_aspartate through the cell wall
Transcription of the aspA, promoted by FecI_a (active)
Translation of aspA
Activation of FecI, induced by the activation of FecR
Activation of FecR induced by FecA-PrhA
Plant cell wall lingand, FecA-PrhA binding

Reactions

The reaction equations for the previous parts, and the reactions rates associated, are summarized in the following table:

#	Reaction	ReactionRate	Active
1	ecoli.ammonia + ecoli.fumarate + ecoli.AAL <-> ecoli.L_aspartate + ecoli.AAL	k1ecoli.ammoniaecoli.fumarateecoli.AAL - k2ecoli.L_aspartate*ecoli.AAL	true
2	ecoli.L_aspartate <-> medium.L_aspartate	kWallDiffusionecoli.L_aspartate - kWallDiffusionBackmedium.L_aspartate	true
3	ecoli.DNAaspA + ecoli.FecI_a -> ecoli.ARNm_aspA + ecoli.DNAaspA + ecoli.FecI_a	kTranscriptecoli.DNAaspAecoli.FecI_a	true
4	ecoli.ARNm_aspA -> ecoli.AAL + ecoli.ARNm_aspA	kTranslation*ecoli.ARNm_aspA	true
5	ecoli.FecR_a + ecoli.FecI <-> ecoli.FecI_a + ecoli.FecR_a	kFecIActivationecoli.FecR_aecoli.FecI - kFecIDeactivationecoli.FecI_aecoli.FecR_a	true
6	ecoli.FecR + ecoli.[ligand:FecA-PrhA] <-> ecoli.FecR_a + ecoli.[ligand:FecA-PrhA]	kFecRActivationecoli.FecRecoli.[ligand:FecA-PrhA] - kFecRDeactivationecoli.FecR_aecoli.[ligand:FecA-PrhA]	true
7	plant_cell_wall.ligand + ecoli.[FecA-PrhA] <-> ecoli.[ligand:FecA-PrhA]	kCellBindingplant_cell_wall.ligandecoli.[FecA-PrhA] - kCellUnbinding*ecoli.[ligand:FecA-PrhA]	true

Team:UPO-Sevilla/Modeling/Signaling

From 2010.igem.org

The signaling circuit

Reactions

Simulations

Analysis

Sensibility

Temporal evolution

Sponsors