Physics Department, Sapienza University of Rome, Roma, Italy.
BMC Evol Biol. 2011 Oct 14;11:301. doi: 10.1186/1471-2148-11-301.
The growth and development of a biological organism is reflected by its metabolic network, the evolution of which relies on the essential gene duplication mechanism. There are two current views about the evolution of metabolic networks. The retrograde model hypothesizes that a pathway evolves by recruiting novel enzymes in a direction opposite to the metabolic flow. The patchwork model is instead based on the assumption that the evolution is based on the exploitation of broad-specificity enzymes capable of catalysing a variety of metabolic reactions.
We analysed a well-studied unicellular eukaryotic organism, S. cerevisiae, and studied the effect of the removal of paralogous gene products on its metabolic network. Our results, obtained using different paralog and network definitions, show that, after an initial period when gene duplication was indeed instrumental in expanding the metabolic space, the latter reached an equilibrium and subsequent gene duplications were used as a source of more specialized enzymes rather than as a source of novel reactions. We also show that the switch between the two evolutionary strategies in S. cerevisiae can be dated to about 350 million years ago.
Our data, obtained through a novel analysis methodology, strongly supports the hypothesis that the patchwork model better explains the more recent evolution of the S. cerevisiae metabolic network. Interestingly, the effects of a patchwork strategy acting before the Euascomycete-Hemiascomycete divergence are still detectable today.
生物有机体的生长和发育反映在其代谢网络中，而代谢网络的进化则依赖于必需的基因复制机制。目前有两种关于代谢网络进化的观点。逆行模型假设途径通过向代谢流相反的方向招募新的酶而进化。而拼凑模型则基于这样的假设，即进化是基于利用能够催化多种代谢反应的广谱特异性酶。
我们分析了一种研究充分的单细胞真核生物 S. cerevisiae，并研究了去除同源基因产物对其代谢网络的影响。我们使用不同的同源和网络定义获得的结果表明，在基因复制确实有助于扩大代谢空间的初始阶段之后，后者达到了平衡，随后的基因复制被用作更专门的酶的来源，而不是新反应的来源。我们还表明，S. cerevisiae 中两种进化策略之间的转变可以追溯到大约 3.5 亿年前。
我们通过一种新的分析方法获得的数据强烈支持了拼凑模型更好地解释了 S. cerevisiae 代谢网络的近期进化的假设。有趣的是，在 Euascomycete-Hemiascomycete 分化之前就已经存在拼凑策略的影响，至今仍能检测到。
