Synthetic genetic circuits using plant protoplasts*

The complexity of plant biology has slowed the development of synthetic gene circuits in plants. However plant synthetic biology can form the basis for sustainable green technologies. The rational design of synthetic networks requires quantitative characterization of components for predictive modeling. This poses special difficulties for plants, since stably transforming plants is time consuming. We developed an experimental system for rapid quantitative measurements of synthetically designed repressors using plant protoplasts but found that protoplast assays show significant experimental batch effects that lead to incorrect quantitative results. With the help of a mathematical model coupled with stochastic simulations, we were successful in explaining and normalizing the batch effects to make quantitative comparisons between different inducible repressors, and approximately predict quantitative properties of synthetic circuits in stably transformed plants. We tested hundreds of repressible promoters, and carried out a statistical analysis of the quantitative data to uncover design principles for building synthetic inducible repressors in plants (Nature Methods, v13, pp94–100, (2016)). Our mathematical model may be broadly applicable to a wider class of cells and assays.