The bigg_e_coli_core Escherichia coli K12
model is a simplified metabolic network model and is (almost) identical to the model published as supporting
material in Orth
et al. (2010). The following exercises are inspired by this document.
- Reset your session
- Pick the bigg_e_coli_core E. coli model from the model and pathway repository
Create a modified model
The idea is to create a new model for the anaerobic growth of E. coli K12:
- Determine the
Reac ID of the boundary reaction for O2
- Export the bigg_e_coli_core model as an Excel spreadsheet (or in any other format but Excel is rather convenient)
- In the enzymes sheet, find the row with the correct
Reac ID, and set the flux boundaries to [0;0] thus preventing O2 from entering or leaving the system
- Save the model in the corresponding format on the user side (with a new name).
- Upload the new model using an informative model identifier, e.g. anaerobic_textbook
- Using the reac_list view,
inspect the original and modified model. Do the two models differ where they are expected to differ?
Flux balance analysis (FBA)
Run FBA on both models.
- Can you identify any changes in the external flux distributions between the two models?
- Can you establish the overall growth stoichiometry for both models.
Are they compatible with E. coli K12 biology?
- Can you identify any internal reactions which change direction?
- What would happen to the FBA solution if all reactions are unconstrained?
Run the reaction knockout analysis on both the aerobic and anaerobic models.
- How many reactions are essential in each model?
- Are there reactions that are essential in one growth condition and not in the other one?
- Are there reactions with beneficial knockout? If so, can you explain why?
A more realistic model
Add the model iAF1260 to your workspace and compare it to the
bigg_e_coli_core model with respect to (1) biomass flux, (2) dead-end
reactions, (3) correlation groups.
Expanding the bigg_e_coli_core model
Insert one or two additional amino acids in the bigg_e_coli_core model.
Don't forget to improve the biomass reaction?