Dataset Information

Feist2007_EcMetabol_flux2

ABSTRACT: organism E. coli K-12 MG1655 model iAF1260 Biomass Objective Function (BOF) Ec_biomass_iAF1260_core_59p81M (E. coli biomass objective function (iAF1260) - core - with 59.81 GAM estimate) flux balance analysis objective maximize BOF Growth Associated Maintenance (GAM) 59.81 mmol ATP gDW-1 Non-Growth Associated Maintenance (NGAM) 8.39 mmol ATP gDW-1 hr-1 media conditions computational minimal media carbon source 11.0 mmol glucose gDw-1 hr-1 aerobic or anaerobic 18.2 mmol O2 gDw-1 hr-1 additional constraints reactions constrained to zero 152 reactions identified to be unavailable to the cell under glucose aerobic conditions flux split between reaction pairs NDH-1:NDH-2 is 1:1 (3 pairs of reactions - different quinone usage) NADH10:NADH17pp, NADH5:NADH16pp, NADH9:NADH18p p This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

SUBMITTER: Molecular Systems Biology

PROVIDER: MODEL3023641273 | BioModels | 2005-01-01

REPOSITORIES: BioModels

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			Action	DRS
	MODEL3023641273?filename=MODEL3023641273-biopax2.owl	Owl
	MODEL3023641273?filename=MODEL3023641273-biopax3.owl	Owl
	MODEL3023641273?filename=MODEL3023641273.m	Other
	MODEL3023641273?filename=MODEL3023641273.pdf	Pdf
	MODEL3023641273?filename=MODEL3023641273.png	Other

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Publications

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Feist Adam M AM Henry Christopher S CS Reed Jennifer L JL Krummenacker Markus M Joyce Andrew R AR Karp Peter D PD Broadbelt Linda J LJ Hatzimanikatis Vassily V Palsson Bernhard Ø BØ

Molecular systems biology 20070626

An updated genome-scale reconstruction of the metabolic network in Escherichia coli K-12 MG1655 is presented. This updated metabolic reconstruction includes: (1) an alignment with the latest genome annotation and the metabolic content of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E. coli and (3) thermodynamic information for the included chemical reactions ...[more]

PMID: 17593909

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Project description:Metabolic cofactors such as NADH and ATP play important roles in a large number of cellular reactions and it is of great interest to dissect the role of these cofactors in different aspects of metabolism. Towards this goal, we overexpressed NADH oxidase and the soluble F1-ATPase in Escherichia coli to lower the level of NADH and ATP, respectively. We used a systems biology approach to study the response to these perturbations by measuring global transcription profiles, metabolic fluxes and the metabolite levels. We integrated information from the different measurements using network-based methods to identify high-scoring networks in a global interaction map that included protein interactions, transcriptional regulation and metabolism. The results revealed that the action of many global transcription factors such as ArcA, Fnr, CRP and IHF commonly involved both NADH and ATP while others were influential only in one of the pertubations. In general, overexpressing NADH oxidase invokes response in widespread aspects of metabolism involving the redox cofactors (NADH and NADPH) while ATPase has a more focused response to restore ATP level by enhancing proton translocation mechanisms and repressing biosynthesis. Interestingly, NADPH played a key role in restoring redox homeostasis through the concerted activity of isocitrate dehydrogenase and UdhA transhydrogenase. We present a reconciled network of regulation that illustrates the overlapping and distinct aspects of metabolism controlled by NADH and ATP. Our study contributes to the general understanding of redox and energy metabolism and should help in developing metabolic engineering strategies in E. coli. The experimental design involves measuring transcriptome in three strains (in triplicates) of E. coli during mid-exponential phase of growth on MOPS media supplemented with glucose. The three strains are: 1. REF: MG1655/pAK80 (MG1655 transformed with a plasmid with no insert) 2. NOX: MG1655/pAC06 (MG1655 transformed with a plasmid containing NADH oxidase) 3. ATPase: MG1655/pCP41 (MG1655 transformed with a plasmid containing soluble ATPase) RNA was extracted using Qiagen RNeasy kit and processes according to AffymetrixÂ® guidelines. The quality of RNA was verified using BioAnalyzer (Agilent BioSystems) and the electropherograms are shown in the file âRNA quality.pdfâ. Samples 1-3 are REF, Samples 4-6 are NOX and Samples 7-9 are ATPase. The fragmented cRNA was hybridized to E. coli Genome 2.0 chips.