生物系统进化优势模式的形成
Formation of Dominant Mode by Evolution in Biological Systems
摘要：
细胞稳定生长对所有细胞组分表达水平变化的限制最近在实验和理论上都进行了讨论。通过假设一个小的环境扰动，并考虑到它的线性响应，一个共同的比例，在这样的表达变化的推导和部分实验数据验证。在这里，我们研究了全球蛋白质表达在${\it Escherichia coli}$在各种环境扰动。值得注意的是，它们在各组成部分之间是成比例的，尽管这些环境变化并不小，而且涵盖了不同类型的应力，而比例系数则对应于生长率的变化。然而，由于这种全球比例并不适用于稳定增长条件下的所有系统，因此需要一个新的概念框架。我们假设这种比例是进化的结果。为了验证这一假设，我们分析了一个细胞模型，该模型具有大量通过催化反应网络自我复制的组分，并证实了所有组分浓度的共同比例是通过进化过程形成的，以在给定的环境条件下最大限度地提高细胞生长（因此适应性）。此外，我们发现，响应于环境和进化变化的所有组分的浓度变化被约束在一个巨大的维状态空间内的一维主轴上。基于这些观察结果，我们提出了一个理论，其中进化后的高维表型变化被限制在与生长速率相关的一维主轴上，这可以解释广泛的实验和数值结果。
英文摘要：
Constraints on changes in expression levels across all cell components imposed by the steady growth of cells have recently been discussed both experimentally and theoretically. By assuming a small environmental perturbation and considering a linear response to it, a common proportionality in such expression changes was derived and partially verified by experimental data. Here, we examined global protein expression in ${\it Escherichia coli}$ under various environmental perturbations. Remarkably they are proportional across components, even though these environmental changes are not small and cover different types of stresses, while the proportion coefficient corresponds to the change in growth rate. However, since such global proportionality is not generic to all systems under a condition of steady growth, a new conceptual framework is needed. We hypothesized that such proportionality is a result of evolution. To validate this hypothesis, we analyzed a cell model with a huge number of components that reproduces itself via a catalytic reaction network, and confirmed that the common proportionality in the concentrations of all components is shaped through evolutionary processes to maximize cell growth (and therefore fitness) under a given environmental condition. Further, we found that the concentration changes across all components in response to environmental and evolutionary changes are constrained along a one-dimensional major axis within a huge-dimensional state space. Based on these observations, we propose a theory in which high-dimensional phenotypic changes after evolution are constrained along a one-dimensional major axis that correlates with the growth rate, which can explain broad experimental and numerical results.
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