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Comparative analysis of M. pneumoniae models using the CytoSEED plugin for metabolic model visualization
Author(s) -
Hazekamp Nicholas Lee,
Kammeraad Joshua,
Bockstege Benjamin,
DeJongh Matthew
Publication year - 2012
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.26.1_supplement.983.4
Subject(s) - pentose phosphate pathway , transaldolase , computational biology , biochemistry , glycolysis , chemistry , biology , metabolism
We have developed a Cytoscape plugin for exploring genome‐scale metabolic models in the Model SEED database ( www.theseed.org/models ). We have used this plugin to compare our metabolic model for Mycoplasma pneumoniae M129 (Mp) with the one published by Yus et al. in Science in 2009. Mp is missing an annotated gene for the transaldolase (TAL) activity, which converts erythrose‐4‐phosphate into sedoheptulose‐7‐phosphate. However, it is known that Mp produces phospho‐ribose‐diphosphate, indicating that the pentose phosphate pathway is functional. The Yus model asserts that the TAL activity is present; however, our software shows that two reactions present in our model associated with fructose‐bisphosphate aldolase and phosphofructokinase bridge this gap using sedoheptulose‐1,7‐bisphosphate as an intermediary compound. Our software also shows differences in asserted transport reactions, glycerophospholipid metabolism, and maintenance of oxidation‐reduction balance. Our software enables comparing the results of flux variability analysis for the two models on different growth media, and the determination of which reactions are essential on the minimal media discovered by Yus et al. NSF 0745100, 0850546