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J Biotechnol. 2014 Aug 20;184:172-8. doi: 10.1016/j.jbiotec.2014.05.021. Epub 2014 Jun 5.

Reducing Recon 2 for steady-state flux analysis of HEK cell culture.

Author information

1
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland, Australia. Electronic address: l.quek@uq.edu.au.
2
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Queensland, Australia.
3
ACIB GmbH, Austrian Centre of Industrial Biotechnology, Vienna, Austria.
4
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.

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.

KEYWORDS:

Flux analysis; Genome-scale model; Human metabolism; Mammalian cell culture; Model reduction

PMID:
24907410
DOI:
10.1016/j.jbiotec.2014.05.021
[Indexed for MEDLINE]
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