title: Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100.
abstract: The γ-proteobacterium Xanthomonas campestris pv. campestris (Xcc) B100 synthesizes the polysaccharide xanthan, a commercially important viscosifier. Since the complete genome of Xcc B100 is available, systems biology tools were applied to obtain a deeper understanding of the metabolism involved in xanthan biosynthesis. A large-scale metabolic network was reconstructed and manually curated. The reconstructed network included 352 genes, 437 biochemical reactions, 10 transport reactions, and 338 internal metabolites. To use this network for flux balance analysis, the biomass composition of Xcc B100 was determined. The comprehensive model obtained was applied for in silico analyses to predict biomass generation and gene essentiality. Predictions were extensively validated by analyzing batch culture performance and by carbon balancing including xanthan production. Single gene deletion mutants causing deficiencies in the central carbohydrate metabolism were constructed to enforce major flux redistributions. The impact of xanthan production was studied in vivo and in silico, comparing the physiology of a gumD mutant, negative in xanthan production, with the original strain. The results indicate a redistribution of resources from xanthan to biomass, rather than a reduction in carbon uptake. With this high quality metabolic model, both systems biology analyses and synthetic biology reengineering of Xcc gained an important tool.
authors: Abteilung für Proteom- und Metabolomforschung, Fakultät für Biologie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany.
authors: Sarah
authors: S
authors: Schatschneider
authors: Marcus
authors: M
authors: Persicke
authors: Steven Alexander
authors: SA
authors: Watt
authors: Gerd
authors: G
authors: Hublik
authors: Alfred
authors: A
authors: Pühler
authors: Karsten
authors: K
authors: Niehaus
authors: Frank-Jörg
authors: FJ
authors: Vorhölter
mesh_terms: D018533:Biomass; D003198:Computer Simulation; D004274:DNA, Recombinant / Q000096:biosynthesis / Q000235:genetics; D005285:Fermentation / Q000235:genetics; D017353:Gene Deletion; D053858:Metabolic Networks and Pathways; D009154:Mutation / Q000235:genetics; D011135:Polysaccharides, Bacterial / Q000235:genetics* / Q000378:metabolism*; D016959:Xanthomonas campestris / Q000235:genetics* / Q000378:metabolism*
chemical_list: D004274:DNA, Recombinant; D011135:Polysaccharides, Bacterial; C002563:xanthan gum
keywords: Central carbon metabolism; Phosphofructokinase; Phosphogluconate dehydrogenase; Phosphoglucose isomerase; Plant pathogen; Transketolase