Towards Engineering a Programmable Universal Transcription Activation System

Developing the next generation of medical, agricultural and sustainability biotechnology is limited by the complexity of natural biological systems; namely the dynamics and interactions between genetically encoded parts. Synthetic biology seeks to reduce the complexity by replacing natural biological components with simplified, synthetic control systems. Transcription is a major control step for biological systems and thus subject to a number of successful efforts for synthetic regulation, primarily in eukaryotes. These systems, however, rely primarily on host components and thus are still largely entangled in the complex host processes. Additionally, prokaryotes, which represent a large fraction of hosts in industrial biotech, still lack the programmable activation systems of eukaryotes. Furthermore components are not readily transferable between the two, which is important for simplifying design. Thus, we sought to design a programmable transcription activation system in prokaryotes by combining the wealth of information on the strong phage T7 RNA Polymerase (RNAP) with modular and programmable DNA binding proteins. Importantly, T7 RNAP is a self-contained RNAP that interacts minimally with the host and is thus orthogonal. We reasoned that reducing T7 RNAPs natural affinity for DNA would allow for control of initiation through programmable DNA binding proteins (DBPs). We show that indeed, T7 RNAP can be programmed to transcribe synthetic promoters via fusion to programmable DNA binding proteins and this interaction can be tuned with various molecular manipulations of promoter and protein. Furthermore, the set of DBPs can be expanded by replacing the fusion with a split T7 and DBP facilitated through programmable leucine zipper domains. This culminates in T7 RNAPs that are programmable and small molecule inducible.Ph.D