Difference between revisions of "Team:Toulouse/Modeling"
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Formate,harmful if to much is produced, is metabolised into others products most of the time. We thus have to find the balance between producing enough formate without | Formate,harmful if to much is produced, is metabolised into others products most of the time. We thus have to find the balance between producing enough formate without | ||
killing Apicoli. | killing Apicoli. | ||
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| − | + | <p class="legend">Figure 3: Reaction catalyzed by PFL</p> | |
Revision as of 14:22, 4 September 2015
Modeling
Content
Metabolic networks
As it has been presented, the aim of our project is to create a biological system able to produce two molecules:
butyric acid and formic acid.
To construct our biological system, we have to introduce a new balance between all metabolic pathways already present in E.Coli.
Indeed, we want to optimize butyrate and formate production in our bacteria with the new pathways we created for ApiColi.
Below are represented all metabolic pathways and metabolites known to date in Escherichia coli K12 MG1655
(most known model). It was obtained from the KEGG database [1].
The first part of this work is to determine the metabolic pathways in which our molecules of interest are taking part, in order to
well immerse ourselves in their roles and effects.
Figure 1:Kegg Metabolic pathways - Escherichia coli K-12 MG1655
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 enzyme 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 enzyme 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 metabolised into others products most of the time. We thus have to find the balance between producing enough formate without killing Apicoli.
Figure 3: Reaction catalyzed by PFL
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. [5] Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJY, Hanai T, Liao JC. 2008. Metabolic engineering of Escherichia coli for 1-butanol production. Metabolic Engineering 10:305–311.
- [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.
