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Team:KU Leuven/Project/Glucosemodel/MeS/Modelling
From 2013.igem.org
Secret garden
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Methylsalicylate - Model
BLABLABLA
Section 1: ODE Representation
The methyl salicylate pathway contains the following reactions:
with:
- PchA = Pyochelin A
- PchB = Pyochelin B
- BSMT1 = Benzoate/Salicylate carboxyl methyltransferase
- SAM = S-adenosyl-L-methionine
- SAH = Salicylate methyl ester
At first, our intention was to model the entire pathway from the implemented DNA sequence to the resulting production rate. This could be very useful in order to have an approximation of the resulting production rate and in order to figure out the rate-limiting step. In order to achieve this we need a mathematical representation of all of our biological processes, the transcription rate, the mRNA degradation rate, the translation rate, the protein degradation rate and the enzyme kinetics.
We created a set of ordinary differential equations (ODEs), which represents every step in our pathway: transcription, translation and the chemical activity of the protein.
mRNA flux:
Comments:
The proteins pyochelin A (PchA) and pyochelin B (PchB) are extracted from the pchDCBA operon and are the structural proteins responsible for salicylate biosynthesis. Serion et al. (1995) describe that expression of the pchA gene appears to depend on the transcription and translation of the upstream pchB gene in P. aeruginosa. They also state “Salicylate formation was demonstrated in an Escherichia coli entC mutant lacking isochorismate synthase when this strain expressed both the pchBA genes, but not when it expressed pchB alone”. This is also confirmed by Gaille, Reimman and Haas (2003): “The pchA gene is strictly co-expressed with the upstream pchB gene; without pchB being present in cis no expression of pchA can be observed”. Finally Serion et al. (1995) also report that the pchB stop codon overlaps the presumed pchA start codon.
Therefore we conclude that transcription and translation of pchA and pchB is coupled and decided to use only one gene (pchBAgene), and only one mRNA molecule (mpchbA) for both proteins (PchA and PchB) in our model.
Protein flux:
Methyl salicylate synthesis:
Comments:
• For our modeling purposes, we take the chorismate concentration as a pool.
• For every reaction we assume Michaelis-Menten kinetics.
• The division by NA. EcoliCellVolume in the numerator is necessary to convert the amount of molecules of our enzyme to a concentration.
• In equations [3.E] and [3.F ] Km3a represents the Km of salicylate while Km3b represents the Km of SAM.
