Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
Nucleic Acids Res. 2021 May 21;49(9):5393-5406. doi: 10.1093/nar/gkab253.
Computations widely exist in biological systems for functional regulations. Recently, incoherent feedforward loop and integral feedback controller have been implemented into Escherichia coli to achieve a robust adaptation. Here, we demonstrate that an indirect coherent feedforward loop and mutual inhibition designs can experimentally improve the fold change of promoters, by reducing the basal level while keeping the maximum activity high. We applied both designs to six different promoters in E. coli, starting with synthetic inducible promoters as a proof-of-principle. Then, we examined native promoters that are either functionally specific or systemically involved in complex pathways such as oxidative stress and SOS response. Both designs include a cascade having a repressor and a construct of either transcriptional interference or antisense transcription. In all six promoters, an improvement of up to ten times in the fold change activation was observed. Theoretically, our unitless models show that when regulation strength matches promoter basal level, an optimal fold change can be achieved. We expect that this methodology can be applied in various biological systems for biotechnology and therapeutic applications.
计算在生物系统中广泛存在，用于功能调节。最近，非相干前馈环和积分反馈控制器已被引入大肠杆菌中，以实现稳健的适应。在这里，我们证明了间接相干前馈环和相互抑制设计可以通过降低基础水平同时保持高最大活性，实验上提高启动子的折叠变化。我们将这两种设计应用于大肠杆菌中的六个不同的启动子，从合成诱导启动子作为原理验证开始。然后，我们检查了在功能上是特定的或系统地参与复杂途径（如氧化应激和 SOS 反应）的天然启动子。这两种设计都包括一个具有抑制剂的级联和转录干扰或反义转录的构建体。在所有六个启动子中，观察到折叠变化激活的提高高达十倍。从理论上讲，我们的无单位模型表明，当调节强度与启动子基础水平匹配时，可以实现最佳的折叠变化。我们期望这种方法可以应用于各种生物技术和治疗应用的生物系统中。
