Regulation of gene expression dynamics by multiple signalling pathways: towards rational design of biological controller

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Sang Yun Lee, A. A. R. Webb, R. J. Tanaka

Imperial College London, United Kingdom

One of the key challenges in construction of synthetic biological networks is to understand the mechanisms that enable the system to process and respond to multiple environmental inputs. Such mechanisms for regulation of gene expression are implemented by appropriate designs of promoter architectures and the upstream regulatory networks. Processing multiple inputs can potentially generate great diversity in the temporal dynamics of the resulting behaviours, contributing to versatility of the system response in constantly changing environmental settings. We take a combined experimental and theoretical approach to investigate the design of both promoter architecture and upstream regulatory network for Response-to-Dehydration 29A (RD29A), a plant stress gene that is inducible by a variety of abiotic stresses: NaCl and ABA. The gene’s inducibility by multiple types of stresses is conferred by its promoter, with presence of non-overlapping binding sites for multiple types of TFs that are regulated by different stress signalling pathways. Our experiments showed clearly distinct temporal expression profiles of RD29A under single NaCl and single ABA stress conditions, and synergistic profile of RD29A expression when exposed simultaneously to the two stresses. We proposed a mathematical model of the upstream regulatory pathways and revealed the underlying mechanisms for these experimentally observed RD29A expression dynamics. The overall expression dynamics of a gene is driven by tight temporal coordination between ‘slow’ transcriptional and ‘fast’ enzymatic signalling pathways while the synergistic temporal expression profile primarily arises from crosstalks in upstream regulatory steps. This observation provides a novel insight as to how the expression dynamics, and thus the response of the gene towards multiple environmental inputs, can be appropriately controlled through rational design of its promoter and upstream regulatory networks. The design principles obtained in this study is expected to be applied to the systems with more than two inputs.