title: Novel approach to engineer strains for simultaneous sugar utilization.
abstract: Use of lignocellulosic biomass as a second generation feedstock in the biofuels industry is a pressing challenge. Among other difficulties in using lignocellulosic biomass, one major challenge is the optimal utilization of both 6-carbon (glucose) and 5-carbon (xylose) sugars by industrial microorganisms. Most industrial microorganisms preferentially utilize glucose over xylose owing to the regulatory phenomenon of carbon catabolite repression (CCR). Microorganisms that can co-utilize glucose and xylose are of considerable interest to the biofuels industry due to their ability to simplify the fermentation processes. However, elimination of CCR in microorganisms is challenging due to the multiple coordinating mechanisms involved. We report a novel algorithm, SIMUP, which finds metabolic engineering strategies to force co-utilization of two sugars, without targeting the regulatory pathways of CCR. Mutants of Escherichia coli based on SIMUP algorithm showed predicted growth phenotypes and co-utilized glucose and xylose; however, consumed the sugars slower than the wild-type. Some solutions identified by the algorithm were based on stoichiometric imbalance and were not obvious from the metabolic network topology. Furthermore, sequencing studies on the genes involved in CCR showed that the mechanism for co-utilization of the sugars could be different from previously known mechanisms.
authors.affiliation: Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, Canada M5S 3E5.
authors.forename: Pratish
authors.initials: P
authors.lastname: Gawand
authors.forename: Patrick
authors.initials: P
authors.lastname: Hyland
authors.forename: Andrew
authors.initials: A
authors.lastname: Ekins
authors.forename: Vincent J J
authors.initials: VJ
authors.lastname: Martin
authors.forename: Radhakrishnan
authors.initials: R
authors.lastname: Mahadevan
mesh_terms: D000465:Algorithms; D048168:Escherichia coli K12 / Q000235:genetics / Q000378:metabolism; D005947:Glucose / Q000235:genetics / Q000378:metabolism; D060847:Metabolic Engineering; D008954:Models, Biological; D009154:Mutation; D014994:Xylose / Q000235:genetics / Q000378:metabolism
chemical_list: D014994:Xylose; D005947:Glucose
keywords: Bilevel optimization; CCR; Carbon catabolite repression; E4P; Erythrose-4-phosphate; Escherichia coli; F6P; Fructose-6-phosphate; G6P; GA3P; Glucose-6-phosphate; Glucose–xylose co-utilization; Glyceraldehydes-3-phosphate; Metabolic modeling; PEP; PPP; PTS; PYR; Pentose phosphate pathway; Phosphoenolpyruvate; Phosphotransferase system; Pyruvate; R5P; Ribose-5-phosphate; Strain design; X5P; Xylulose-5-phosphate