Team:UChile OpenBio-CeBiB/Model/Results
Results
From the previous procedures, we obtained the following results:
Phase 1: The First Approach
Metabolic Pathway
We observed the production of Glucose 6-phosphate, and an increased of the intermediaries affected by FBP/SBPase. Aditionally, all the compounds reach the steady state with concentrations close to reallity, but the timeline should be reviewed. We considered this model correct for a first approach.
Genetic Pathway
The graphic shows the increase of FBP/SBPasa enzyme, which confirm the expected results. If we expand the timeline, we could observed the steady state.
Metabolic Pathway, B12 Absent
Metabolic Pathway, B12 Present
We observed that in absence of B12, the steady state is reached after than in the case of presence of the vitamin. Besides, in the first graph there is an initial accumulation of UDP-Glucose, which in the second scenario is null due to the full production of starch.
Genetic Pathway, B12 Absent
Genetic Pathway, B12 Present
We observed the same behavior of STA1 and STA6 for both cases, therefore insensitive to B12 vitamin. For GBS2 we observed the expected behavior, having a null production of protein, due to the production of antisense RNA, which is confirmed with the formation of double strand DNA.
Phase 2: Sensitivity Analysis
G6P Production from Calvin Cycle
For G6P production from Calvin Cycle, it is possible to highlight six Michaelis Menten constants important to consider. This process is most influenced by the F6P-G6P conversion, given it is a reversible reaction. This makes it possible to optimize the cycle in order to determine the best set of parameters to fully achieve maximum carbon uptake, which would then allow us to evaluate the possibility of including new catalysis mechanisms regarding these reactions. Additionally, we have to notice that the majority of the sensitive parameters do not increase the concentration of G6P in steady state given the variation of their values, but instead they actually decrease this amount. Therefore, it may occur that the upper limit of G6P production (which correlates directly to carbon fixation) is already given by the chosen set of parameters. As a summary, the key reaction is the reversible conversion of fructose-6-phosphate to glucose-6-phosphate.
Starch Production from Antisense
We can observe that the reactions concerning the molecule glucose-6-phosphate are the most sensitive for optimization. Regarding the Michaelis Menten constant of the enzymes, there was no considerable variation in the STA1/STA6 (in this case, STA denotes both enzymes). This could occur due to precision problems with the algorithm and the software sensitivity to extremely low numbers. Considering this, it is necessary to take into account the three enzyme's kinetic parameters for the subsequent optimization
G6P Production from Calvin Cycle
Virtually, the same conclusions from the Michaelis Menten constants of the Calvin Cycle are reached, except for the conversion of G6P-F6P, where in this case it is not absurdly more heavy in influence than the other parameters.
Starch Production from Antisense
In this case, exactly the same conclusions as the corresponding Michaelis Menten constants are drawn.
G6P Production from Calvin Cycle
Starch Production from Antisense
Here we see that the degradation rate of G6P, UDPG, and Starch are the most relevant in the circuit. However, modifying these values is somewhat difficult unless an additional enzyme to increase stability of the mentioned compounds is inserted. Therefore, these parameters wouldn't be transcendental for the optimization, but their value must still be determined by model fitting.
GBS2 effect on Starch Production
STA1 effect on Starch Production
STA6 effect on Starch Production
It is pretty evident that the system is heavily affected by GBS2, and the other enzymes have little influence. The supposed reason was mentioned earlier: the algorithms and software may not be sensitive to low values of initial conditions, though the circuit could actually just be chaotic. Nevertheless, it is necessary to consider these parameters for the three enzymes in order to properly optimize the starch synthesis pathway control.
