E. coli FAQs
Most often the questions we receive about E. coli modeling can be answered by examining the publication:
Becker, S.A., Feist, A.M., Mo, M. L., Hannum, G., Palsson, B.Ø., Herrgard, M.J. "Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox" Nat. Protocols 2, 727-738 (2007).
and questions about a reconstruction itself can be answered by examining the publication:
Reed, J.L., Famili, I., Thiele, I., and Palsson, B.Ø., "Towards multidimensional genome annotation", Nature Reviews Genetics, 7(2):130-41 (2006).
Other Frequently Asked Questions
Q: How do I optimize for biomass?
A: One way is to include a reaction in the S matrix that consumes the biomass constituents from the network in the appropriate ratios and then optimize for this one flux.
Q: I don't get any growth from simulation. Why is that?
A: There could be several reasons for it. First, check that exchange fluxes are implemented correctly. Allow the fluxes of NH4, SO4, O2, phosphate, water and proton (if using iJR904), Fe, K, Na, CO2. Next, check if you can make basic precursors from glucose. Then, add a temporary reaction that drain each precursor and maximize for this temporary reaction. Finally, check that you can make each of the biomass constituents. Once you identify which ones you cannot make, you need to go through the metabolic routes and determine why.
Q: How come there are extracellular versions of compounds but not intracellular compounds?
A: It's because some transport reactions change the compound, for example, from glucose to glucose-6-phosphate.
Q: What is the difference between a transport reaction and an exchange reaction?
A: The difference lies in a boundary. Whereas the boundary of a transport reaction is a cell membrane, an exchange reaction's boundary is a system boundary.
Q: Are there any values available that I can compare my model's results with?
A: The following table has some simulation results using iJR904. Substrate uptake rates were simulated with a max of 10 mmol/gDWhr.
| Substrate | Condition | Growth rate (hr-1) |
|---|---|---|
| acetate | aerobic | 0.19964 |
| glucose | aerobic | 0.92195 |
| glucose | anaerobic | 0.21625 |
| succinate (BOF) | aerobic | 0.43287 |
Optimal flux distributions for the iAF1260 model are included in the supplemental material (see 'SBML File Properties' for constraints, pg. 4) and can be downloaded here:
supp info: http://www.nature.com/msb/journal/v3/n1/extref/msb4100155-s2.pdf
SBML files: http://www.nature.com/msb/journal/v3/n1/extref/msb4100155-s6.zip