Witting Michael
Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
Chair of Analytical Food Chemistry, TU München, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany.
Metabolites. 2020 Mar 28;10(4):130. doi: 10.3390/metabo10040130.
Genome scale metabolic models (GSMs) are a representation of the current knowledge on the metabolism of a given organism or superorganism. They group metabolites, genes, enzymes and reactions together to form a mathematical model and representation that can be used to analyze metabolic networks in silico or used for analysis of omics data. Beside correct mass and charge balance, correct structural annotation of metabolites represents an important factor for analysis of these metabolic networks. However, several metabolites in different GSMs have no or only partial structural information associated with them. Here, a new systematic nomenclature for acyl-based metabolites such as fatty acids, acyl-carnitines, acyl-coenzymes A or acyl-carrier proteins is presented. This nomenclature enables one to encode structural details in the metabolite identifiers and improves human readability of reactions. As proof of principle, it was applied to the fatty acid biosynthesis and degradation in the consensus model WormJam.
基因组规模代谢模型（GSMs）是对特定生物体或超生物体新陈代谢当前知识的一种表示。它们将代谢物、基因、酶和反应组合在一起，形成一个数学模型和表示形式，可用于在计算机上分析代谢网络或用于组学数据分析。除了正确的质量和电荷平衡外，代谢物的正确结构注释是分析这些代谢网络的一个重要因素。然而，不同GSMs中的几种代谢物没有或只有部分与之相关的结构信息。在此，提出了一种针对基于酰基的代谢物（如脂肪酸、酰基肉碱、酰基辅酶A或酰基载体蛋白）的新系统命名法。这种命名法使人们能够在代谢物标识符中编码结构细节，并提高反应的人类可读性。作为原理证明，它被应用于共识模型WormJam中的脂肪酸生物合成和降解。
