Reprogramming the plant form: Using synthetic signalling to study and re-engineer development

Human society is dependent on plant products for essentials such as food, textiles, lumber and pharmaceuticals. However, due to a rapidly changing agricultural environment and a steadily increasing demand for resources, we face a future where access to these essentials may be severely curtailed. One strategy to address these challenges is to develop tools that allow us to rationally re-engineer plants to be more productive and robust. In this work, we present a set of strategies to re-engineer development using synthetic signaling systems to alter how plants interpret and respond to hormonal cues, specifically of the plant hormone auxin, which plays a central role in development. We demonstrate how synthetic auxin-sensitive promoters can be used in conjunction with mathematical modeling to rationally alter a range of developmental processes, such as phyllotaxy, in Arabidopsis thaliana. To address the weaknesses of this approach, namely the lack of tissue specificity and fine grain tunability of auxin sensitivity, we developed a novel class of auxin-degradable CRISPR-based transcription factors (ADCTFs). We demonstrate that our modular ADCTF platform has the potential to tunable regulate genes based on endogenous auxin fluxes. It could also be used to visualize the fluxes of auxin during development, in ways that complement existing reporters, to further elucidate the role of these fluxes in development. Future applications of this technology include the rapid domestication of wild plants by making them less bushy and making plants with programmable root architectures for drought resistance.