Modeling
Background
We have successfully inserted the pathway for xylose utilization into our engineered S. cerevisiae and observed its assimilation of xylose and the production of X-5-P, which can be directly converted to S-7-P, the precursor to all MAAs we wished to produce. However, we want to investigate further the relationship between X-5-P and S-7-P under various glucose-xylose proportions.
Partnership with Greatbay_SCIE
Greatbay_SCIE has team members that are very skillful and experienced in building models, so we achieved a partnership where they aided us in writing the equations for the model and we researched the parameters of the ODEs that they wrote for us.
Hugo from LINKS_China communicating with Tom from Greatbay_SCIE about the model
To view more about our partnership with SCIE, please visit the partnership page.
Design
Our model is a simulation of the xylose and glucose utilization pathway and the PPP cycle of our engineered S. cerevisiae with TAL1 deleted. We wrote specific ODEs for each enzyme-substrate reaction to demonstrate the effect of different glucose-xylose proportions.
Overview of the pathway that our model simulated. Arrows represent reactions. Yellow circles represent enzymes. Blue circles represent substrates and products for the reactions.
Aims
Our mathematical model has two major aims:
1. To find the minimal glucose-xylose proportion that possesses a sufficient amount of glucose to satisfy S. cerevisiae's energy demand for glycolysis so that all xylose will be utilized for the production of S-7-P.
2. To verify a phenomenon we observed in the lab: S. cerevisiae with TAL1 deleted and Xyl 1, Xyl 2, and Xyl 3 transformed into it grows better in pure glucose but needs xylose to produce MAAs.
Modeling Process - Glucose Part
The target molecule we are trying to obtain is S7P, and there are 2 pathways that eventually lead to S7P: one from glucose and one from xylose.
The glucose part of our model begins with the conversion of glucose into G-6-P by HK, modeled by the equation:
ODE for G-6-P; Vmax8: HK; Km8: glucose
Then, we move along the pathway of glucose metabolism by converting G-6-P into either F-6-P by PGI:
ODE for F-6-P; Vmax1: PGI; Km1: G-6-P
Or 6PGL by lactonase:
ODE for 6PGL; Vmax4: lactonase; Km4: G-6-P
F-6-P Route
F-6-P is either joined with GA-3-P and converted into E4P by TK1 in the bi-substrate reaction:
ODE for E4P; Vmax17: TK1; Km18: GA-3-P; Km19: E4P
Or converted into DHAP by PFK and ALD:
ODE for F1, 6-BP; Vmax9: PFK; Km9: F-6-P
ODE for DHAP; Vmax7: ALD; Km7: F1, 6-BP
Then, E4P and DHAP are converted into S7P by ALD and S-1, 7-BPP:
ODE for S-1, 7-BP; Vmax18: ALD; Km20: DHAP; Km21: E4P
ODE for S7P; Vmax3: S-1, 7-BPP; Km3: S-1, 7-BP
6PGL Route
6PGL is converted into Ru5P by G6PDH and 6PGDH:
ODE for 6PG; Vmax10: G6PDH; Km10: 6PGL
ODE for Ru5P; Vmax11: 6PGDH; Km11: 6PG
Then, Ru5P is converted into X5P and R5P by PPPE and PPI respectively:
ODE for X5P; Vmax6: PPPE; Km6: Ru5P
ODE for R5P; Vmax5: PPPI; Km5: Ru5P
Then, X5P and R5P are converted into S7P by TK in a bi-substrate reaction:
ODE for S7P; Vmax16: TK; Km16: R5P; Km17: X5P
Modeling Process - Xylose Part
Xylose is converted into X5P by Xyl1, Xyl2, and Xyl3:
ODE for xylitol; Vmax12: Xyl1; Km12: xylose
ODE for xylulose; Vmax13: Xyl2; Km13: xylitol
ODE for X5P; Vmax14: Xyl3; Km14: xylulose
Then, X5P and R5P from the glucose pathway are converted into S7P:
ODE for S7P; Vmax16: TK; Km16: R5P; Km17: X5P
Discussions & Looking into the Future
Due to time limitations and technical difficulties in researching parameters, our model failed to produce any reliable results. However, we do have a clearer understanding of the effect of deleting TAL1 and inserting the xylose metabolism pathway into our engineered S. cerevisiae after making the model.
After the wiki freeze, we will improve our model by searching for more relevant and accurate parameters. After our model succeeds in the future, we will find the perfect glucose-xylose ratio for the production of our MAAs. This will help us achieve maximum efficiency in the large-scale manufacturing of UV-PRISMA.
Parameters List
Parameters