Team:UPF CRG Barcelona/Simulation
SIMULATION OF INTESTINAL CONDITIONS
In the set of our project, it is highly important to know in which environment the genetically modified bacteria is going to be working. In the intestine there is a steep gradient for oxygen; its concentrations decrease precipitously to near anoxia at the midpoint of the lumen [1]. For this reason, if we want our engineered bacteria to properly work in the gut, it has to work under anaerobic conditions as well. However, long chain fatty acids (LCFA) are degraded via the beta-oxidation pathway, an aerobic pathway for excellence, therefore it is necessary to find alternative strategies in order to metabolize LCFA in absence of oxygen.
Moreover, when engineering a pathway in order to optimize it, it is very important to keep in mind that the overall efficiency of the synthetic pathway can decrease either by the loss of metabolic intermediates by diffusion or by competing pathways [2]. In the intestine, after diet ingestion, there is going to be other energetic substrates aside of LCFA, especially sugars and amino acids. Therefore, most of the catabolic pathways of bacteria are going to be active and can interfere with beta oxidation efficiency. For this reason, it is very important to study the metabolic network as a whole instead of only focusing on the pathway that we want to modify. In order to do so, we performed flux balance analysis simulations to be able to predict PA uptake and bacteria growth taking into account all the aforementioned variables.
References
[1] Espey, M. (2013). Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota. Free Radical Biology and Medicine, 55, pp.130-140.
[2] Na, D., Kim, T. and Lee, S. (2010). Construction and optimization of synthetic pathways in metabolic engineering. Current Opinion in Microbiology, 13(3), pp.363-370.