Tanaka Michihiro, Yamada Takuji, Itoh Masumi, Okuda Shujiro, Goto Susumu, Kanehisa Minoru
Bioinformatics center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
Genome Inform. 2006;17(1):230-9.
Recent evidence points to the existence of scale-free properties in many biological networks. By topological analysis, several models including preferential attachment and hierarchical modules have been proposed to explain how these networks are organized. On the other hand, analyses using dynamics have suggested that gene expression and metabolic networks have been organized with the scale-free property by the other models such as "rich-travel-more" and "log-normal dynamics." Because most of these approaches are based on comparative genomics of extant species, and did not consider evolutionary events such as horizontal gene transfer, gene loss and gene gain, we have analyzed transition of metabolic networks from the vertical point of view of evolution. First, to identify metabolic networks of common ancestors, we applied a parsimony algorithm for the enzymatic reaction set. Then by comparing the estimated metabolic networks among common ancestors, we investigated the transition of metabolic networks along the evolutionary process. As a result, we estimated enzymatic reaction contents of 227 common ancestors from 228 extant species, and found that links of several specific metabolites have frequently changed during the course of evolution.
最近的证据表明，许多生物网络中存在无标度特性。通过拓扑分析，已经提出了包括偏好依附和层次模块在内的几种模型来解释这些网络是如何组织的。另一方面，动力学分析表明，基因表达和代谢网络是通过“富者更富”和“对数正态动力学”等其他模型以无标度特性组织起来的。由于这些方法大多基于现存物种的比较基因组学，没有考虑水平基因转移、基因丢失和基因获得等进化事件，我们从进化的垂直角度分析了代谢网络的转变。首先，为了识别共同祖先的代谢网络，我们对酶促反应集应用了简约算法。然后，通过比较共同祖先之间估计的代谢网络，我们研究了代谢网络在进化过程中的转变。结果，我们估计了来自228个现存物种的227个共同祖先的酶促反应内容，发现几种特定代谢物的连接在进化过程中经常发生变化。
