title: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
abstract: 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. The conversion of this metabolic network reconstruction into an in silico model is detailed. A new step in the metabolic reconstruction process, termed thermodynamic consistency analysis, is introduced, in which reactions were checked for consistency with thermodynamic reversibility estimates. Applications demonstrating the capabilities of the genome-scale metabolic model to predict high-throughput experimental growth and gene deletion phenotypic screens are presented. The increased scope and computational capability using this new reconstruction is expected to broaden the spectrum of both basic biology and applied systems biology studies of E. coli metabolism.
authors.affiliation: Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Feist
authors.forename: Christopher S
authors.initials: CS
authors.lastname: Henry
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Reed
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Andrew R
authors.initials: AR
authors.lastname: Joyce
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
authors.forename: Linda J
authors.initials: LJ
authors.lastname: Broadbelt
authors.forename: Vassily
authors.initials: V
authors.lastname: Hatzimanikatis
authors.forename: Bernhard Ø
authors.initials: BØ
authors.lastname: Palsson
mesh_terms: D000465:Algorithms; D018533:Biomass; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030541:Databases, Genetic; D004734:Energy Metabolism; D048168:Escherichia coli K12 / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics; D008954:Models, Biological; D016366:Open Reading Frames / Q000235:genetics*; D013816:Thermodynamics
chemical_list: D005947:Glucose