Team:Tartu TUIT/Model
Project: Yeasthylene
The demand on ethylene has only been increasing during the last decade. It is used as an essential building block in many chemical compounds.The main aim of our project is to find an alternative and biological way of producing ethylene. That is why we have decided to genetically engineer yeast cells to produce ethylene from sucrose.
Modelling
For modelling we used the SimBiology toolbox provided by Mathworks for iGEM teams. Below you can see the diagram made in SimBiology using the common drag-and-drop mode:
As our project idea is to split functions between two yeast strains so as to reduce metabolic burden, it’s only logical to model two different compartments, referred to in the above graph as strainA and strainB. Unfortunately, due to time constraints, we weren’t successful in fully modelling the whole glycolysis and TCA (tricarboxylic acid) cycle pathways, here each illustrated as only one reaction. For this reason, our result may not be as accurate as we’d like it to be.
Most of the enzyme kinetic constants were taken from the BRENDA website.
The following ODEs were calculated after providing the kinetic laws for each reaction in the SimBiology model:
First we simulated a batch mode of cultivation without air supply (Figure 1) and, even though our model does not seems to comply with reality (arginine concentration reaching 0 mol/L), we could infer that: (1) feeding glutamate (arginine precursor) would not only increase the availability of arginine itself, but also possibly increase the 2-oxoglutarate for the ethylene production; (2) providing a constant air supply would be better as oxygen levels drops over time; and (3) as apparently the glucose and fructose do not reach high concentrations (are readily consumed by strain A) and as Saccharomyces cerevisiae is a Crabtree positive organism, this could hinder ethanol production. Therefore, we decided to base our model on a fed-batch or chemostat bioreactor cultivation, providing constant supplies of glutamate, oxygen, and sucrose (Figure 2).
Figure 1. Simulation using a batch cultivation model
Figure 2. Simulation using a bioreactor operated in fed-batch or chemostat mode
After doing so, our ethylene production was markedly improved (Figure 2). Connecting this result to our lab work we have concluded that ethylene yield would be increased by using chemostat bioreactor cultivation.
