Team:Evry/interactions

From 2013.igem.org

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<h3>Question 1: Interractions between the artifitial system and the metabolism of <i>E. coli</i></h3>
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<em>Model</em> : <i>E. coli</i> iJR904 with addition of ENTSYNTH and ENTOUT reactions.
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<p>
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In order to test whether the system interacts with the metabolism of the bacteria we applied the FBA with a modification to the objective function:
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<img src="https://static.igem.org/mediawiki/2013/2/28/Optim_q1.png" alt="fba optimization function for testing q1" />
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<p>
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By varying i between 0 and 1 we can vary the contributions of enterobacting production and biomass growth.
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<h3>Simulation</h3>
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<p>
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The <a href="#Fig3">Figure 3</a> presents the results of the simulation following the previous settings.
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<a title="Nom Lien" href="https://static.igem.org/mediawiki/2013/8/80/Q1_curve.png">
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<img alt="Nom Lien" src="https://static.igem.org/mediawiki/2013/8/80/Q1_curve.png" alt="Considered E.Coli Metabolic Reaction Network." class="Picture"/>
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<b>Figure 3:</b> <p>Fluxes as function of the i coefficient of the modified objective function. Dotted lines : Important fluxes; Solid lines : Reactions belonging to the ENTEROBACTIN biosynthesis pathway; Dashed lines : Other reactions consuming important metabolites.</p>
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<a id="Fig3"></a>
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<ul>
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<li>Setup : i varied from 0 to 1 with a step of 0.01.</li>
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<li>The code for this model can be found at the bottom of the page</li>
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</ul>
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</p>
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<h3>Interpretation</h3>
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<p>
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The graph is divided in two parts :
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<h4>i < 0.303</h4>
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In this part, no ENTOUT flux is present, hence there is no production of enterobactin. In the other hand there are two non-zero constant fluxes, the CHORISMATE MUTASE (at 0.28 mmol/gDW/h) and DEOXYCHORISMATE SYNTHASE (at 0.04 mmol/gDW/h). The objective function is linearly decreasing with i meaning that the system does not change in this part.
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<h4>i = 0.303</h4>
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For this value of i there is a brutal change in the different fluxes :
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<ul>
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<li>CHORMISMATE MUTASE flux goes to 0 mmol/gDW/h</li>
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<li>DEOXYCHORISMATE SYNTHASE flux goes to 0 mmol/gDW/h</li>
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<li>ISOCHORISMATE SYNTHASE, ISOCHORISMATASE, ENTOUT fluxes goes to their maximal values 2.1 mmol/gDW/h</li>
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</ul>
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The objective function f stops decreasing.
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<h4>i > 0.303</h4>
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After this value of i the system stays the same as proved by the linear increase of the objective function with i.
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<h3>Conclusion</h3>
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<p>
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The production of enterobactin modifies the flux distribution for only two reactions out of 5 (the others have a nul flux) : CHORMISMATE MUTASE and DEOXYCHORISMATE SYNTHASE.<br/>
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Thus <em>there is an interaction between the enterobactin production system and the <i>E. coli</i> metabolism</em> that happen at the level of these reactions.
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Revision as of 15:47, 26 October 2013

Iron coli project

Question 1: Interractions between the artifitial system and the metabolism of E. coli

Model : E. coli iJR904 with addition of ENTSYNTH and ENTOUT reactions.

In order to test whether the system interacts with the metabolism of the bacteria we applied the FBA with a modification to the objective function:

fba optimization function for testing q1

By varying i between 0 and 1 we can vary the contributions of enterobacting production and biomass growth.

Simulation

The Figure 3 presents the results of the simulation following the previous settings.

Nom Lien
Figure 3:

Fluxes as function of the i coefficient of the modified objective function. Dotted lines : Important fluxes; Solid lines : Reactions belonging to the ENTEROBACTIN biosynthesis pathway; Dashed lines : Other reactions consuming important metabolites.

  • Setup : i varied from 0 to 1 with a step of 0.01.
  • The code for this model can be found at the bottom of the page

Interpretation

The graph is divided in two parts :

i < 0.303

In this part, no ENTOUT flux is present, hence there is no production of enterobactin. In the other hand there are two non-zero constant fluxes, the CHORISMATE MUTASE (at 0.28 mmol/gDW/h) and DEOXYCHORISMATE SYNTHASE (at 0.04 mmol/gDW/h). The objective function is linearly decreasing with i meaning that the system does not change in this part.

i = 0.303

For this value of i there is a brutal change in the different fluxes :

  • CHORMISMATE MUTASE flux goes to 0 mmol/gDW/h
  • DEOXYCHORISMATE SYNTHASE flux goes to 0 mmol/gDW/h
  • ISOCHORISMATE SYNTHASE, ISOCHORISMATASE, ENTOUT fluxes goes to their maximal values 2.1 mmol/gDW/h
The objective function f stops decreasing.

i > 0.303

After this value of i the system stays the same as proved by the linear increase of the objective function with i.

Conclusion

The production of enterobactin modifies the flux distribution for only two reactions out of 5 (the others have a nul flux) : CHORMISMATE MUTASE and DEOXYCHORISMATE SYNTHASE.
Thus there is an interaction between the enterobactin production system and the E. coli metabolism that happen at the level of these reactions.

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