Difference between revisions of "Team:Toulouse/Modeling"
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To construct our biological system, we have to introduce a new balance between all metabolic pathways already present in <i>E.Coli</i>. | To construct our biological system, we have to introduce a new balance between all metabolic pathways already present in <i>E.Coli</i>. | ||
| − | Indeed, we want to <b>optimize</b> butyrate and formate | + | Indeed, we want to <b>optimize</b> butyrate and formate productions 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 | + | Below are represented all metabolic pathways and metabolites known to date in <i>Escherichia coli</i> K12 MG1655 |
(most known model). It was obtained from the KEGG database <a target="_blank" href="http://www.kegg.jp/kegg-bin/highlight_pathway?scale=0.5&map=eco01100&keyword=">[1]</a>.<br> | (most known model). It was obtained from the KEGG database <a target="_blank" href="http://www.kegg.jp/kegg-bin/highlight_pathway?scale=0.5&map=eco01100&keyword=">[1]</a>.<br> | ||
| − | The first part of this work is to determine the metabolic pathways in which | + | The first part of this work is to determine the metabolic pathways in which both molecules of interest are taking part, in order to |
well immerse ourselves in their roles and effects. | well immerse ourselves in their roles and effects. | ||
</p> | </p> | ||
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<p align="justify" style="font-size:15px;"> | <p align="justify" style="font-size:15px;"> | ||
Formate is already produced by <i>E.coli</i>, in our project we need Apicoli to produce more. To optimize biosynthesis we had | Formate is already produced by <i>E.coli</i>, in our project we need Apicoli to produce more. To optimize biosynthesis we had | ||
| − | to study all the genes coding for | + | 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. | this enzyme provoke the degradation of pyruvate producing formate. | ||
</p> | </p> | ||
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<p align="justify" style="font-size:15px;"> | <p align="justify" style="font-size:15px;"> | ||
The subnetwork presented below is the result of this mapping, it was realised with the | The subnetwork presented below is the result of this mapping, it was realised with the | ||
| − | MetExplore platform <a target="_blank" href="http://metexplore.toulouse.inra.fr/joomla3/index.php">[2]</a> and present all known | + | MetExplore platform <a target="_blank" href="http://metexplore.toulouse.inra.fr/joomla3/index.php">[2]</a> 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. | 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 | + | 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. | killing Apicoli. | ||
</p> | </p> | ||
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<center> | <center> | ||
<img src="https://static.igem.org/mediawiki/2015/5/5c/TLSE_model_fig3.png" style="width:100%;"/> | <img src="https://static.igem.org/mediawiki/2015/5/5c/TLSE_model_fig3.png" style="width:100%;"/> | ||
| − | <p class="legend">Figure 3: Metabolic network of all | + | <p class="legend">Figure 3: Metabolic network of all reactions involving formate happening in <i>E.coli</i></p></center> |
<div class="subtitle"> | <div class="subtitle"> | ||
| Line 135: | Line 135: | ||
<div class="group center"> | <div class="group center"> | ||
<p align="justify" style="font-size:15px;">To help ourselves creating Apicoli we modelised our system by using Flux Balance | <p align="justify" style="font-size:15px;">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 <i>E.coli</i> | + | Analysis (FBA) and Flux Variability Analysis (FVA). We used the most recent described model for <i>E.coli</i> K12 MG1655, describing all metabolic pathways known |
and up to date. This <a target="_blank" href="https://2015.igem.org/File:TLSE_EC_iJO1366_modified_XML_model.zip">XML</a> file</p> | and up to date. This <a target="_blank" href="https://2015.igem.org/File:TLSE_EC_iJO1366_modified_XML_model.zip">XML</a> file</p> | ||
</div> | </div> | ||
Revision as of 12:25, 7 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 productions 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 both 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 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. [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.
