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首页> 外文期刊>Journal of Molecular Biochemistry >The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism
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The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism

机译：代谢基因型空间的组织有助于氮代谢的适应性进化

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摘要

A metabolism is a complex chemical reaction system, whose metabolic genotype – the DNA encoding the enzymes catalyzing these reactions – can be compactly represented by its complement of metabolic reactions. Here, we analyze a space of such metabolic genotypes. Specifically, we study nitrogen metabolism and focus on nitrogen utilization phenotypes that are defined through the viability of a metabolism – its ability to synthesize all essential small biomass precursors – on a given combination of sole nitrogen sources. We randomly sample metabolisms with known phenotypes from metabolic genotype space with the aid of a method based on Markov Chain Monte Carlo sampling. We find that metabolisms viable on a given nitrogen source or a combination of nitrogen sources can differ in as much as 80 percent of their reactions, but can form networks of genotypes that are connected to one another through sequences of single reaction changes. The reactions that cannot vary in any one metabolism differ among metabolisms, and include a small core of “absolutely superessential” reactions that are required in all metabolisms we study. Only a small number of reaction changes are needed to reach the genotype network of one metabolic phenotype from the genotype network of another metabolic phenotype. Our observations indicate deep similarities between the genotype spaces of macromolecules, regulatory circuits, and metabolism that can facilitate the origin of novel phenotypes in evolution.
机译：代谢是一个复杂的化学反应系统，其代谢基因型-编码催化这些反应的酶的DNA-可以由其代谢反应的补充来紧凑地表示。在这里，我们分析这种代谢基因型的空间。具体来说，我们研究氮的代谢，着重研究氮的利用表型，该表型是通过新陈代谢的生存能力（即其合成所有必需的小生物量前体的能力）在唯一的氮源组合中定义的。我们借助基于马尔可夫链蒙特卡洛采样的方法，从代谢基因型空间中随机抽取具有已知表型的代谢。我们发现，在给定氮源或氮源组合上可行的新陈代谢可在其反应中发生多达80％的差异，但可形成基因型网络，这些基因型通过单个反应变化序列相互连接。在任何一种新陈代谢中不能改变的反应在新陈代谢中是不同的，并且包括我们研究的所有新陈代谢中所必需的“绝对必要”反应的小核心。从另一种代谢表型的基因型网络到一种代谢表型的基因型网络只需要少量的反应变化。我们的观察结果表明，大分子的基因型空间，调节回路和代谢之间的相似性很高，可以促进进化中新表型的起源。

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