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Analysis of the Whole System
Testing the models of separate sub-systems is a useful technique for understanding how different elements of the process work and interact with each other. However, in this project we are interested in the electron output of the whole electron transfer system in E. Coli. This is exactly the topic of our discussion in this page.
Varying the Glucose input
The input of the whole electron transfer system is glucose. Hence, it is only logical to ask the following question: How does varying the glucose input affect the electron output.
Figure set 1. Electron output given different amounts of glucose. The images used in the .gif can be downloaded from here.
Figure set 1 shows that varying the glucose input has almost no effect on the electron output. This leads us to the assumption that there is some sort of limiting factor inside the system. We already saw that increasing the amount of NapC increases the electron output (This can be seen in the analysis of the sub-models). But is NapC the bottleneck we are looking for? Or is NapC only a limiting factor when we consider the periplasmic part of the system on its own?
Varying the amount of Complex I and Complex II
In this case we get interesting results. Consider the following sets of images:
Figure set 2. Varying the amount of Complex I. The images used in the .gif can be downloaded from here.
Figure set 3. Varying the amount of Complex II. The images used in the .gif can be downloaded from here.
The above results are enough for us to conclude that Complex I and Complex II are indeed limiting factors for the electron transfer system. However, the question remains: Is NapC a limiting factor as well?
Varying the amount of NapC
Observing the behaviour of the electron transfer system when varying the amount of NapC gives us the following result:
Figure set 4. Varying the amount of NapC. The images used in the .gif can be downloaded from here.
Here we can clearly see that NapC, at quantities over 20 micromoles, does not significantly affect the output of the system. This, in conjunction with our sub-model analysis which indicated that NapC is the major limiting factor for periplasmic transfer, shows that Complex I and II are the bottlenecks for the complete system.
If this limitation were to be solved and the electron output of the TCA cycle increased, then NapC would likely become the new bottleneck of the entire model.
Varying the amount of flavins
Figure set 5. Varying the amount of flavins. The images used in the .gif can be downloaded from here.
Flavins, as can be seen in Figure set 5, do not play a crucial role in the electron transfer when we consider the whole system. But, just like NapC, when their amount is varied in their corresponding sub-system, flavins act as a bottle neck (This can be seen on the previous page of the Kappa modelling.).
Varying the amount of insoluble iron
Figure set 6. Varying the amount of insoluble iron. The images used in the .gif can be downloaded from here.
Figure set 6 shows the electron output of the system when we vary the amount of insoluble iron. We can see that the electron output changes almost insignificantly. This means that the amount of insoluble iron plays little role on the electron transfer process.
Conclusion
EdiGEM's Kappa modelling investigates the relation between various elements of the electron transfer system in E. coli within the system as a whole and with respect to their immediate "neighbours". We found out that Complex I, complex II, Napc and flavins are potential bottle necks for the system.
In the future, as more information on the system becomes available, more accurate models can be made in order the confirm our results. In addition, more work can be done on the analysis of other periplasmic elements in the system.
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