title: Use of flux pre-analysis to enable ¹³C tracer studies in pyruvate kinase-deficient Escherichia coli.
abstract: Pyruvate kinase-deficient Escherichia coli (PB25) is a low by-product-producing yet fast-growing mutant that has been shown to have technological potential. Determining the flux limits through finding the extreme point flux sets was previously reported to identify alternate metabolite trafficking scenarios. Previously, the extreme point flux sets were used to design tracer experiments; however, variation in extracellular measurements was not considered, and reaction reversibility was assumed to be low to moderate. In this study, we examined the utility of limiting the fluxes and predetermining the trafficking scenarios in PB25, including confirmation of quasi-linearity between extreme points to ensure sensitivity is maintained. The effects of variation in extracellular measurements and reaction reversibilities were also examined. Tightened flux limits reduced the nonlinearity between label distribution and fluxes. For low to moderate reversibility, contrast was also preserved. However, for highly reversible phosphoglucoisomerase activity, information from common analytes could lead to a flux solution that is biased towards one extreme point. Based on the PB25 model, some suggestions are provided for how predetermining flux limits and trafficking scenarios could enable flux identification in larger network problems.
authors.affiliation: Carnegie Mellon University, Department of Chemical Engineering, Pittsburgh, PA 15213, USA. jwmeade@andrew.cmu.edu
authors.forename: Jonathan
authors.initials: J
authors.lastname: Meade
authors.forename: Saleem
authors.initials: S
authors.lastname: Khan
authors.forename: Mohammad
authors.initials: M
authors.lastname: Ataai
authors.forename: Michael
authors.initials: M
authors.lastname: Domach
mesh_terms: D000085:Acetates / Q000378:metabolism; D057486:Carbon Cycle; D002250:Carbon Radioisotopes / Q000032:analysis; D018929:Cell Culture Techniques; D003198:Computer Simulation; D004926:Escherichia coli / Q000378:metabolism*; D005947:Glucose / Q000378:metabolism*; D019344:Lactic Acid / Q000378:metabolism; D053858:Metabolic Networks and Pathways; D008962:Models, Theoretical; D011770:Pyruvate Kinase / Q000172:deficiency* / Q000235:genetics; D011849:Radioactive Tracers
chemical_list: D000085:Acetates; D002250:Carbon Radioisotopes; D011849:Radioactive Tracers; D019344:Lactic Acid; D011770:Pyruvate Kinase; D005947:Glucose