Studying the metabolic perturbations

Question

Are there any interractions between our synthetic construction E. coli central metabolism ?

Observation

If the ENTx genes present on our constructions are expressed, it will increase the quantity of the corresponding enzymes in the bacteria. More enzymes mean more consumption pressure on all the metabolites of the ENTEROBACTIN production pathway. As seen on Figure 1, two metabolites could be subject to this effect : CHORISMATE and ISOCHORISMATE.

Figure 1:

The ENTEROBACTIN production pathway (cyan) and the other metabolic reactions consuming the same metabolites (red). circles : enzymes name.

The ISOCHORISMATE case

The ISOCHORISMATE metabolite is only consumed by one other metabolic reaction catalyzed by the MenD enzyme. The Figure 2 presents the metabolic map conaining the reaction catalyzed by MEND.

Figure 2:

The metabolic map containing the pathway menD belongs to.

As one can see, the menD enzyme is used upstream of the VITAMIN K cycle. It is interesting because vitamins are always produced in small quantities as they are toxic for the cell. With this observation we can deduce that menD should be present in small quantities inside the cell and thus should not use too much of the produced ISOCHORISMATE.

The CHORISMATE case

There are different pathways consuming this metabolite, some could be neglected in the same manner as the menD pathway presented above. But others are part of the central metabolism of E. coli. The enzymes which associated reaction consume chorismate are the following:

• TrpE : which belongs to tryptophan biosynthesis pathway, and thus to E. coli central metabolism. This reaction should have a non-null flux when doing FBA simulations.
• UbiC : which belongs to the ubiquinone biosynthesis pathway, a coenzyme used in the aerobic cellular respiration. This reaction may have a null flux in the FBA simulation as it does not directly participate to the metabolic function of the cell.
• PabA/B : which belongs to the 4-AMINOBENZOATE biosynthesis pathway, which is used in the production of the folic acid, which is a vitamin. This reaction may have a null flux in the FBA simulation also.
• PheA/B : which belongs to the tyrosine and phenylalanine biosynthesis pathways which belongs to E. coli central metabolism. This flux should not be null in the FBA simulation.

Setup

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:

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.

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.