Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA.
Nat Commun. 2021 Jan 12;12(1):325. doi: 10.1038/s41467-020-20094-3.
A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.
向工程生物系统迈进的关键一步是能够精确调节对环境刺激的遗传反应。在大肠杆菌诱导启动子的情况下，我们对序列组成和基因表达之间关系的理解不完整，阻碍了我们可预测地控制转录反应的能力。在这里，我们对 8269 个经过合理设计的 IPTG 诱导启动子的表达动态进行了分析，这些启动子共同探索了 RNA 聚合酶和 LacI 阻遏物结合位点强度的个体和组合效应。然后，我们拟合了一个统计力学模型来测量表达，该模型可以准确地对基因表达进行建模，并揭示理论上最优诱导启动子的特性。此外，我们还研究了三种替代的启动子结构，并表明在启动子内重新定位结合位点会影响观察到的启动子元件之间的组合效应类型。总的来说，这种方法使我们能够分解诱导启动子元件之间的关系，并发现具有理想特性的工程诱导启动子的实用见解。
