New E. coli central metabolism model published.

Posted on: March 9, 2017

PLOS Computational Biology just published a new paper by Millard et al. containing the most complete model of Escherichia coli's central metabolism, to date.

Millard P, Smallbone K, Mendes, P (2017) Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PloS Computational Biology 13(2):e1005396

This E. coli model contains 3 compartments (environment, periplasm and cytoplasm), 62 metabolites, and 68 reactions. It includes the following pathways:

The model couples these pathways in a way that allows balancing the concentrations of cofactors (ATP/ADP/AMP, NAD(P)(H) and FAD(H2)) and simulate energy and redox metabolism. The model also includes a reaction representing growth, which ensures that the building blocks are consumed in stoichiometric proportions fixed by the cell composition, and not independently from each other.

The model is available in SBML format from the BioModels database as MODEL1505110000, or from the paper's supplementary data (in both SBML and COPASI formats). The model was validated with a large set of experimental data (not used to calibrate it), which is included in the paper and its supplementary information.

The model was then used to inquire about the extent to which metabolic regulation (enzyme kinetics and feedback, eg. through allosteric regulation) controls metabolism, versus how much of that contribution comes from the actual network stoichiometry or from gene regulation. The results strongly suggest that most of the observed behaviour derives from metabolic regulation.

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