SLIMEr：使用改进的基于约束的建模框架探究酵母中脂质代谢的灵活性
SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.
作者信息
Sánchez Benjamín J, Li Feiran, Kerkhoven Eduard J, Nielsen Jens
机构信息
Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
出版信息
BMC Syst Biol. 2019 Jan 11;13(1):4. doi: 10.1186/s12918-018-0673-8.
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 .
背景
在基因组规模代谢模型（GEMs）中，一个反复出现的问题是由于单个脂质种类的众多可能组合以及相应的完全详细数据的缺乏，难以将脂质正确表示为生物量需求。在本研究中，我们提出了SLIMEr，这是一种使用常见实验数据在GEMs中正确表示脂质需求的形式主义方法。
结果
SLIMEr通过数学构建增强了GEM，除了对脂质类别和酰基链分布的约束外，我们将脂质拆分为可测量实体（SLIME反应）。通过在酿酒酵母的共识GEM上实施SLIMEr，我们可以表示脂质种类的准确数量，分析所得分布的灵活性，并计算从一种代谢状态转变为另一种代谢状态的能量成本。
结论
该方法显示出在不同条件下更好地理解酵母脂质代谢的潜力。SLIMEr可在https://github.com/SysBioChalmers/SLIMEr上免费获取。
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