title: A Method to Constrain Genome-Scale Models with 13C Labeling Data.
abstract: Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America.
authors.forename: Héctor García
authors.initials: HG
authors.lastname: Martín
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America.
authors.forename: Vinay Satish
authors.initials: VS
authors.lastname: Kumar
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America.
authors.forename: Daniel
authors.initials: D
authors.lastname: Weaver
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America.
authors.forename: Amit
authors.initials: A
authors.lastname: Ghosh
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America.
authors.forename: Victor
authors.initials: V
authors.lastname: Chubukov
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America.
authors.forename: Aindrila
authors.initials: A
authors.lastname: Mukhopadhyay
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Department of Bioengineering, University of California, Berkeley, Berkely, United States of America.
authors.forename: Adam
authors.initials: A
authors.lastname: Arkin
authors.affiliation: Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America; Department of Bioengineering, University of California, Berkeley, Berkely, United States of America; Department of Chemical Engineering, University of California, Berkeley, Berkeley, United States of America.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
mesh_terms: D000465:Algorithms; D002247:Carbon Isotopes / Q000378:metabolism*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D055786:Gene Knockout Techniques; D016680:Genome, Bacterial / Q000235:genetics; D060847:Metabolic Engineering; D064688:Metabolic Flux Analysis / Q000379:methods*; D008954:Models, Biological; D049490:Systems Biology / Q000379:methods*
chemical_list: D002247:Carbon Isotopes