Team:TU Delft/Modeling/MFA

From 2010.igem.org

Revision as of 19:13, 25 October 2010 by Jcnossen (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

Metabolic Flux Analysis

A metabolic flux analysis (MFA) is an analysis to calculate the theoretical maximal yields for a proposed system of pathways in a micro-organism. Several product pathways were introduced to the metabolic network of E. coli along with the hydrocarbon degradation from our BioBricks to see what the maximal theoretical yields on alkanes are compared to glucose.

Are you not familiar with a metabolic flux analysis? Read more about how a metabolic flux analysis works.

For our MFA a Matlab application, CellNetAnalyzer (CNA), was used. CNA already contains a simplified E. coli metabolic network. This network was slightly changed and hydrocarbon degradation was added to it. The resulting network is the network is the construct as it was intended in our project. To investigate the potential of this system to make something useful of the alkanes several product pathways were added the E. coli metabolic network in silico. We also describe how the network was generated.

The fluxes that were calculated for maximal yields with CellNetAnalyzer were exported and inputted into Omix. Omix is a tool for drawing networks in general, but lends itself espescially well for biochemical pathways. From the networks that were drawn with Omix we made a tool in which you yourself can select different substrates and products and see what pathways are used in an ideal situation. The tool is below this text. The selectable substrates are glucose, dodecane (C₁₂-alkane) and tridecane (C₁₃-alkane). The selectable outputs are, biomass growth, NO₃ electron acceptor, PHB, isoprene and hydrogen. With biomass growth and NO₃ as electron acceptor the fluxes are optimized towards biomass production. Biomass is produced using the 12 key metabolites as precursors. The key metabolites have a red color. The substances with a yellow color are extracellular. For the three other outputs, PHB, isoprene and hydrogen, the fluxes are optimized towards production of these substances. The numbers next to some of the reactions in the tool are the EC numbers of the corresponding enzymes.