SLIMEr: Probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework
Journal article, 2019

Background: A 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. Results: SLIMEr 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. Conclusions: The approach shows potential for better understanding lipid metabolism in yeast under different conditions. SLIMEr is freely available at https://github.com/SysBioChalmers/SLIMEr.

Genome-scale metabolic modeling

Saccharomyces cerevisiae

Lipidomics

Flux balance analysis

Author

Benjamín José Sánchez

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Feiran Li

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Eduard Kerkhoven

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Technical University of Denmark (DTU)

BMC Systems Biology

1752-0509 (ISSN)

Vol. 13 1 4

Subject Categories

Computational Mathematics

Biophysics

Bioinformatics (Computational Biology)

DOI

10.1186/s12918-018-0673-8

PubMed

30634957

More information

Latest update

2/12/2019