Large-scale reconstruction and phylogenetic analysis of metabolic environments
Large-scale reconstruction and phylogenetic analysis of metabolic environments
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DOI：
10.1073/pnas.0806162105
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发表时间：
2008-09-23
影响因子：
11.1
通讯作者：
Ruppin, Eytan
中科院分区：
文献类型：
--
作者：
Borenstein, Elhanan;Kupiec, Martin;Ruppin, Eytan
代谢网络的拓扑结构不仅可以为物种的代谢能力提供重要的见解，还可以为它们进化的栖息地提供重要的见解。在这里，我们介绍了代谢网络的“种子集”的概念——一组化合物，基于网络拓扑结构，是外生获得的——并提供了一个方法框架来计算推断给定网络的种子集。这些种子群形成了代谢网络与其周围环境之间的生态“界面”，近似于每个物种的有效生化环境。分析了478种植物的代谢网络，并确定了每种植物的种子集，对这种预测的代谢环境进行了全面的大规模重建。种子的组成与物种环境的几个基本特征显著相关，并与主要适应性的生物学观察相一致。环境高度可预测的物种（如专性寄生虫）往往比生活在可变环境中的物种拥有更小的种子。种子组的系统发育分析揭示了整个系统发育树中控制种子增益和损失的复杂动力学以及种子和非种子化合物之间的过渡过程。我们的研究结果表明，种子状态是短暂的，种子要么从网络中完全脱落，要么相对较快地成为非种子化合物。种子组也允许一个成功的重建系统发育树的生命。提出的“逆向生态学”方法为大规模研究生物与其栖息地之间的进化相互作用奠定了基础。
The topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. Here we introduce the concept of a metabolic network's "seed set"-the set of compounds that, based on the network topology, are exogenously acquired-and provide a methodological framework to computationally infer the seed set of a given network. Such seed sets form ecological "interfaces" between metabolic networks and their surroundings, approximating the effective biochemical environment of each species. Analyzing the metabolic networks of 478 species and identifying the seed set of each species, we present a comprehensive large-scale reconstruction of such predicted metabolic environments. The seed sets' composition significantly correlates with several basic properties characterizing the species' environments and agrees with biological observations concerning major adaptations. Species whose environments are highly predictable (e.g., obligate parasites) tend to have smaller seed sets than species living in variable environments. Phylogenetic analysis of the seed sets reveals the complex dynamics governing gain and loss of seeds across the phylogenetic tree and the process of transition between seed and non-seed compounds. Our findings suggest that the seed state is transient and that seeds tend either to be dropped completely from the network or to become non-seed compounds relatively fast. The seed sets also permit a successful reconstruction of a phylogenetic tree of life. The "reverse ecology" approach presented lays the foundations for studying the evolutionary interplay between organisms and their habitats on a large scale.