Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs
Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs
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花青素途径进化的计算模型：偏差、热点和权衡
DOI：
10.1093/icb/icz049
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发表时间：
2019
影响因子：
2.6
通讯作者：
Smith, S. D.
中科院分区：
文献类型：
--
作者：
Wheeler, L. C.;Smith, S. D.
代谢途径的改变是新表型进化的常见机制。花的颜色是复杂表型中代谢进化重要性的一个引人注目的例子，其中基础途径活性的变化导致了多种色素的产生。尽管实验工作已经确定了导致颜色转变的常见突变类别，但我们缺乏将途径功能和活性与不同色素表型进化联系起来的统一模型。创建这种模型的一个挑战是色素途径的分支结构，这可能会由于共享底物的竞争而导致进化权衡。为了预测酶功能和活性变化对色素产生的影响，我们创建了一个主要植物色素沉着途径的简单动力学模型：花青素途径。该模型描述了蓝色、紫色和红色三类花青素色素的生产，因此包括多个分支和底物竞争。我们首先使用一组简单的参数研究了该模型的一般行为。然后，我们随机地演化出一条通向定义的最佳值的路径，并分析了固定突变的模式。这种方法使我们能够量化路径状态空间中轨迹的概率密度，并识别变化的类型和数量。最后，我们检查了我们的模拟结果是否与实验观察结果定性一致，即通过改变途径中分支基因的功能来改变颜色的突变的优势。这些分析提供了一个理论框架，可用于预测新突变在色素表型和多效性方面的后果。
The alteration of metabolic pathways is a common mechanism underlying the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentation pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple, and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a naïve set of parameters. We then stochastically evolved the pathway toward a defined optimum and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examined whether our simulated results qualitatively align with experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework that can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.