Team:KU Leuven/Project/Modelling/Cellular Level

From 2013.igem.org

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  • A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
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Synthetic biology designs new networks within and on top of the existing cellular network of your favourite organism. The key question, however, is whether the cell/tissue/organism will actually be able to produce this network?! Hence, several questions arise on our way to this goal:

- Are there sufficient tRNAs to build these new proteins, or should we codon optimise our strains?
- Will the cell be able to funnel off enough precursor material to build significant amounts of this new network?
- Will the series of proteins and enzymes produce our final, desired product?
- Won’t the cell make toxic side-products in the process, possibly reducing growth and thus production rate?

The answer to these questions lies in modelling but also in designing the appropriate wet-lab experiments to support, verify and improve our modelling.

On a cellular level, we used 2 modelling suites to obtain more insight in our BanAphids. First we worked out the Flux Balance Analysis for methyl salicylate and secondly we employed a Kinetic Parameter Model for methyl salicylate. Obviously, both suites can be used to verify E-beta-farnesene production and limits while other iGEM teams can fill in their favourite compound!

Flux Balance Analysis: Methyl Salicylate

We checked whether the growth rate of our BanAphids will be affected when we introduce our methyl salicylate system. For this, we ran the Flux Balance Analysis using the COBRA Toolbox for MATLAB.

Kinetic Parameters Model: Methyl Salicylate

We have modelled the production system of methyl salicylate by using the transcription, translation and protein degradation rates in order to calculate the mRNA and protein fluxes. We also brought the kinetics of methyl salicylate synthesis into account.

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