title: Reducing Recon 2 for steady-state flux analysis of HEK cell culture.
abstract: A representative stoichiometric model is essential to perform metabolic flux analysis (MFA) using experimentally measured consumption (or production) rates as constraints. For Human Embryonic Kidney (HEK) cell culture, there is the opportunity to use an extremely well-curated and annotated human genome-scale model Recon 2 for MFA. Performing MFA using Recon 2 without any modification would have implied that cells have access to all functionality encoded by the genome, which is not realistic. The majority of intracellular fluxes are poorly determined as only extracellular exchange rates are measured. This is compounded by the fact that there is no suitable metabolic objective function to suppress non-specific fluxes. We devised a heuristic to systematically reduce Recon 2 to emphasize flux through core metabolic reactions. This implies that cells would engage these dominant metabolic pathways to grow, and any significant changes in gross metabolic phenotypes would have invoked changes in these pathways. The reduced metabolic model becomes a functionalized version of Recon 2 used for identifying significant metabolic changes in cells by flux analysis.
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland, Australia. Electronic address: l.quek@uq.edu.au.
authors.forename: Lake-Ee
authors.initials: LE
authors.lastname: Quek
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland, Australia.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Dietmair
authors.affiliation: ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.
authors.forename: Michael
authors.initials: M
authors.lastname: Hanscho
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland, Australia.
authors.forename: Verónica S
authors.initials: VS
authors.lastname: Martínez
authors.affiliation: ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria; Institute for Applied Microbiology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.
authors.forename: Nicole
authors.initials: N
authors.lastname: Borth
authors.affiliation: Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland, Australia.
authors.forename: Lars K
authors.initials: LK
authors.lastname: Nielsen
mesh_terms: D015894:Genome, Human; D057809:HEK293 Cells / Q000378:metabolism*; D006801:Humans; D066298:In Vitro Techniques; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways
keywords: Flux analysis; Genome-scale model; Human metabolism; Mammalian cell culture; Model reduction