Qian Yili, Huang Hsin-Ho, Jiménez José I, Del Vecchio Domitilla
Department of Mechanical Engineering, Massachusetts Institute of Technology , 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.
Faculty of Health of Medical Sciences, University of Surrey , Guildford, Surrey GU2 7XH, U.K.
ACS Synth Biol. 2017 Jul 21;6(7):1263-1272. doi: 10.1021/acssynbio.6b00361. Epub 2017 Apr 3.
A common approach to design genetic circuits is to compose gene expression cassettes together. While appealing, this modular approach is challenged by the fact that expression of each gene depends on the availability of transcriptional/translational resources, which is in turn determined by the presence of other genes in the circuit. This raises the question of how competition for resources by different genes affects a circuit's behavior. Here, we create a library of genetic activation cascades in E. coli bacteria, where we explicitly tune the resource demand by each gene. We develop a general Hill-function-based model that incorporates resource competition effects through resource demand coefficients. These coefficients lead to nonregulatory interactions among genes that reshape the circuit's behavior. For the activation cascade, such interactions result in surprising biphasic or monotonically decreasing responses. Finally, we use resource demand coefficients to guide the choice of ribosome binding site and DNA copy number to restore the cascade's intended monotonically increasing response. Our results demonstrate how unintended circuit's behavior arises from resource competition and provide a model-guided methodology to minimize the resulting effects.
设计基因回路的一种常见方法是将基因表达盒组合在一起。虽然这种模块化方法很有吸引力，但它面临着一个挑战，即每个基因的表达取决于转录/翻译资源的可用性，而这又反过来由回路中其他基因的存在所决定。这就引出了一个问题，即不同基因对资源的竞争如何影响回路的行为。在这里，我们在大肠杆菌中创建了一个基因激活级联文库，在其中我们明确调整每个基因的资源需求。我们开发了一个基于希尔函数的通用模型，该模型通过资源需求系数纳入资源竞争效应。这些系数导致基因之间产生非调节性相互作用，从而重塑回路的行为。对于激活级联，这种相互作用会导致令人惊讶的双相或单调递减响应。最后，我们使用资源需求系数来指导核糖体结合位点和DNA拷贝数的选择，以恢复级联预期的单调递增响应。我们的结果证明了资源竞争如何导致回路产生意外行为，并提供了一种模型指导的方法来最小化由此产生的影响。
