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A hierarchical model of metabolic machinery based on the kcore decomposition of plant metabolic networks

机译:基于植物代谢网络kcore分解的代谢机制层次模型

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摘要

Modeling the basic structure of metabolic machinery is a challenge for modern biology. Some models based on complex networks have provided important information regarding this machinery. In this paper, we constructed metabolic networks of 17 plants covering unicellular organisms to more complex dicotyledonous plants. The metabolic networks were built based on the substrate-product model and a topological percolation was performed using the kcore decomposition. The distribution of metabolites across the percolation layers showed correlations between the metabolic integration hierarchy and the network topology. We show that metabolites concentrated in the internal network (maximum kcore) only comprise molecules of the primary basal metabolism. Moreover, we found a high proportion of a set of common metabolites, among the 17 plants, centered at the inner kcore layers. Meanwhile, the metabolites recognized as participants in the secondary metabolism of plants are concentrated in the outermost layers of the network. This data suggests that the metabolites in the central layer form a basic molecular module in which the whole plant metabolism is anchored. The elements from this central core participate in almost all plant metabolic reactions, which suggests that plant metabolic networks follows a centralized topology.
机译:对代谢机制的基本结构建模是现代生物学面临的挑战。一些基于复杂网络的模型提供了有关此机制的重要信息。在本文中,我们构建了包含单细胞生物的17种植物到更复杂的双子叶植物的代谢网络。基于底物-产物模型建立代谢网络,并使用kcore分解进行拓扑渗滤。代谢物在整个渗滤层的分布显示出代谢整合层次和网络拓扑之间的相关性。我们显示,集中在内部网络中的代谢物(最大kcore)仅包含主要基础代谢的分子。此外,我们在17种植物中发现了一组较高比例的常见代谢产物,它们集中在内部核心层。同时,被认为是植物次生代谢参与者的代谢物集中在网络的最外层。该数据表明中心层中的代谢物形成了基本的分子模块,整个植物的新陈代谢都被锚定在该模块中。这个中心核心的元素几乎参与了所有植物的代谢反应,这表明植物的代谢网络遵循集中化的拓扑结构。

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