imPR90068

We have developed a genome-scale isotope mapping model, imPR90068, based on the iAF1260 metabolic reconstruction of Escherichia coli. The model maps 90,068 non-hydrogen atoms and spans 1,039 metabolites, 2,077 reactions and contains a total of 1.37 x 10¹⁵⁷ isotopomers including 8.34 x 10^{93 13}C isotopomers. These atom mappings trace the path of all non-hydrogen elements including C, O, N, P, S atoms and metal/non-metal ions. The maximum common subgraph (MCS) method coupled with a modified branch and bound algorithm for clique finding was customized to automatically generate these mappings. The mappings obtained for each reaction were pruned to retain only the biochemically relevant ones. Specifically, several symmetry considerations were addressed before the final reaction atom mappings were formulated, including equivalent oxygen atoms (such as those present in carboxyl and phosphate groups), rotationally symmetric molecules (e.g., succinate), metabolites containing a prochiral carbon center (e.g. citrate) or metabolites with a center of inversion but lacking a rotational axis of symmetry. This procedure can be efficiently leveraged for genome-scale models of other organisms to create isotope mapping databases. Common reactions already present in iAF1260 can be directly culled from the imPR90068 reaction-mappings database thus significantly reducing the effort needed to construct other organism-specific mapping models.

We would like to thank Jon Pey and Dr. Francisco J. Planes from CEIT and University of Navarra for bringing to our attention a number of inconsistancies that we have fixed in the updated version.

Ravikirthi, P., Suthers, P.F. and C.D. Maranas (2011), "Construction of an E. Coli Genome-scale Atom Mapping Model for MFA Calculations," Biotechnology and Bioengineering, accepted.

The model is licensed under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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