Identifying Competition Phenotypes in Synthetic Biochemical Circuits
Identifying Competition Phenotypes in Synthetic Biochemical Circuits
复制标题
综合生化回路中竞争表型的识别
DOI：
10.1109/lcsys.2022.3186840
复制
发表时间：
2022-06-28
影响因子：
3
通讯作者：
Sontag, Eduardo D.
中科院分区：
文献类型：
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作者：
Ali Al-Radhawi, M.;Del Vecchio, Domitilla;Sontag, Eduardo D.
合成基因回路需要细胞资源，而细胞资源通常是有限的。这导致了不同基因对资源的竞争，从而改变了合成基因回路的行为。然而，竞争影响行为的方式取决于“瓶颈”资源的身份，这可能很难从投入产出数据中辨别出来。在这封信中，我们的目的是对生物化学回路中资源竞争的数学结构进行分类。我们发现一些竞争结构可以通过它们对不同竞争者或资源水平的反应来区分。具体地说，我们证明了一些响应曲线总是线性的、凸的或凹的。此外，某些资源的高水平保护行为免受低竞争的影响，而其他资源则不然。我们还表明，竞争表型对各种干预的反应不同。在基于给定数据构建模型时，可以使用这种差异来消除候选竞争机制。另一方面，我们表明不同的网络可以显示数学上相等的竞争表型。
Synthetic gene circuits require cellular resources, which are often limited. This leads to competition for resources by different genes, which alter a synthetic genetic circuit's behavior. However, the manner in which competition impacts behavior depends on the identity of the "bottleneck" resource, which might be difficult to discern from input-output data. In this letter, we aim at classifying the mathematical structures of resource competition in biochemical circuits. We find that some competition structures can be distinguished by their response to different competitors or resource levels. Specifically, we show that some response curves are always linear, convex, or concave. Furthermore, high levels of certain resources protect the behavior from low competition, while others do not. We also show that competition phenotypes respond differently to various interventions. Such differences can be used to eliminate candidate competition mechanisms when constructing models based on given data. On the other hand, we show that different networks can display mathematically equivalent competition phenotypes.