title: Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth.
abstract: A model-based analysis is conducted to investigate metabolism of Shewanella oneidensis MR-1 strain in aerobic batch culture, which exhibits an intriguing growth pattern by sequentially consuming substrate (i.e., lactate) and by-products (i.e., pyruvate and acetate). A general protocol is presented for developing a detailed network-based dynamic model for S. oneidensis based on the Lumped Hybrid Cybernetic Model (L-HCM) framework. The L-HCM, although developed from only limited data, is shown to accurately reproduce exacting dynamic metabolic shifts, and provide reasonable estimates of energy requirement for growth. Flux distributions in S. oneidensis predicted by the L-HCM compare very favorably with (13)C-metabolic flux analysis results reported in the literature. Predictive accuracy is enhanced by incorporating measurements of only a few intracellular fluxes, in addition to extracellular metabolites. The L-HCM developed here for S. oneidensis is consequently a promising tool for the analysis of intracellular flux distribution and metabolic engineering.
authors.affiliation: School of Chemical Engineering, Purdue University, West Lafayette, IN, USA.
authors.forename: Hyun-Seob
authors.initials: HS
authors.lastname: Song
authors.forename: Doraiswami
authors.initials: D
authors.lastname: Ramkrishna
authors.forename: Grigoriy E
authors.initials: GE
authors.lastname: Pinchuk
authors.forename: Alexander S
authors.initials: AS
authors.lastname: Beliaev
authors.forename: Allan E
authors.initials: AE
authors.lastname: Konopka
authors.forename: James K
authors.initials: JK
authors.lastname: Fredrickson
mesh_terms: D000332:Aerobiosis / Q000502:physiology; D019149:Bioreactors / Q000382:microbiology*; D049109:Cell Proliferation; D003198:Computer Simulation; D008657:Metabolic Clearance Rate; D008954:Models, Biological; D010100:Oxygen / Q000378:metabolism*; D010101:Oxygen Consumption / Q000502:physiology*; D020592:Shewanella / Q000166:cytology* / Q000502:physiology*
chemical_list: D010100:Oxygen