Journal
BMC SYSTEMS BIOLOGY
Volume 13, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s12918-018-0673-8
Keywords
Genome-scale metabolic modeling; Saccharomyces cerevisiae; Lipidomics; Flux balance analysis
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Funding
- European Union's Horizon 2020 research and innovation program [686070]
- Knut and Alice Wallenberg Foundation
- Novo Nordisk Foundation
- CONICYT [6222/2014]
- Aforsk Foundation
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BackgroundA recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due to the numerous of possible combinations of individual lipid species and the corresponding lack of fully detailed data. In this study we present SLIMEr, a formalism for correctly representing lipid requirements in GEMs using commonly available experimental data.ResultsSLIMEr enhances a GEM with mathematical constructs where we Split Lipids Into Measurable Entities (SLIME reactions), in addition to constraints on both the lipid classes and the acyl chain distribution. By implementing SLIMEr on the consensus GEM of Saccharomyces cerevisiae, we can represent accurate amounts of lipid species, analyze the flexibility of the resulting distribution, and compute the energy costs of moving from one metabolic state to another.ConclusionsThe approach shows potential for better understanding lipid metabolism in yeast under different conditions. SLIMEr is freely available at https://github.com/SysBioChalmers/SLIMEr.
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