Team:Toulouse/Modeling

iGEM Toulouse 2015

Modeling

Content

Metabolic networks

As said before, the aim of our project is to create a biological system able to produce two molecules: butyric acid and formic acid.
To achieve this, we need to modify the existing balance between the metabolic pathways present in E.Coli. Indeed, we want to optimize butyrate and formate productions in our bacterium by adjusting environmental conditions in order to obtain the desired concentrations of the associated acids. The following metabolic network represents all of the known metabolites and metabolic pathways for Escherichia coli K12 MG1655(best known model). It was obtained from KEGG database [1].
Our first step was to identify the pathways in which our molecules take part, in order to have a clear understanding of their role and effect.

Figure 1: Kegg Metabolic pathways - Escherichia coli K-12 MG1655

Formate network

Formate is already produced by E.coli, in our project we need Apicoli to produce more. To optimize biosynthesis we had to study all the genes coding for enzymes involved in this pathway. We focused ourselves on the Pyruvate Formate Lyase (PFL), this enzyme provoke the degradation of pyruvate producing formate.

Figure 2: Reaction catalyzed by PFL

The subnetwork presented below is the result of this mapping, it was realised with the MetExplore platform [2] and present all known enzymes from the Kegg and ByoCyc databases involved with the production or consumption of formate. This map will help us predict the consequences of formate overproduction in Apicoli. Formate, harmful if to much is produced, is metabolized into others products most of the time. We thus have to find the balance between producing enough formate without killing Apicoli.

Figure 3: Metabolic network of all reactions involving formate happening in E.coli

Butyrate network

Flux Balance Analysis (FBA)

Presentation

To help ourselves creating Apicoli we modelised our system by using Flux Balance Analysis (FBA) and Flux Variability Analysis (FVA). We used the most recent described model for E.coli K12 MG1655, describing all metabolic pathways known and up to date. This XML file

Annexes

References

[1] KEGG Metabolic pathways - Escherichia coli K-12 MG1655
[2] Le Conte Y, Arnold G, Trouiller J, Masson C, Chappe B, Ourisson G. 1989. Attraction of the parasitic mite varroa to the drone larvae of honey bees by simple aliphatic esters. Science 245:638–639.
[3] Methods for attracting honey bee parasitic mites. [accessed 2015 Jul 24].
[4] Louis P, Flint HJ. 2009. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol. Lett. 294:1–8.
[6] Wallace KK, Bao Z-Y, Dai H, Digate R, Schuler G, Speedie MK, Reynolds KA. 1995. Purification of Crotonyl-CoA Reductase from Streptomyces collinus and Cloning, Sequencing and Expression of the Corresponding Gene in Escherichia coli. European Journal of Biochemistry 233:954–962.