The hormone auxin controls numerous plant growth- and developmental processes, including many traits of agronomic importance in crops. Thus, engineering endogenous auxin activity has tremendous potential for changing plant architecture by design. Yet this potential remains untapped due to pleiotropic effects associated with altering auxin levels. Auxin signals are locally translated to gene expression changes underlying growth and development by ARF transcription factors, whose DNA-binding mechanisms have recently been uncovered. In this project, I will engineer DNA-binding specificity in the Arabidopsis ARF5 protein to rewire endogenous auxin responses. Firstly, by systematically replacing DNA-contacting amino acids, I will generate mutant proteins with novel or altered DNA-binding specificity. This resource will help reveal the elusive “code” underlying specific protein-DNA interactions and target gene selection. Secondly, by introducing modified ARF5 into Arabidopsis, I will determine how intrinsic protein properties translate to DNA-binding properties in native chromatin, and in addition determine the developmental consequences of rewiring endogenous auxin response. Since variation in auxin response is expected to generate useful phenotypic variation in crops, I will identify induced mutations and standing variation in DNA-contacting residues in the cucumber, tomato and Chrysanthemum ARF5 orthologue. Analyzing DNA-binding specificity of such mutant ARF5 proteins, as well as phenotypic analysis of the mutant plants, will provide an important proof of concept for inducing plant developmental alterations through targeted modification of ARF-DNA interactions, heralding the foundation for plant shape by design.

Plants use solar energy to synthesize sugars and this is the basis for most of life on Earth. Plants are extremely sensitive to light and specialized photoreceptors direct plant development to optimize light capture. Red-, far-red- and blue-light sensitive photoreceptors are well-studied. Surprisingly, even though green light effectively drives plant development, a green light photoreceptor remains unknown. In this project, we aim to illuminate the mechanism by which plants sense and respond to green light and how these responses foster plant performance in green-rich (shaded) environments. We hypothesize that the relatively unknown, chloroplast localized cryptochrome3 (cry3) is a green light photoreceptor. Importantly, we recently discovered that green light inhibits seedling greening via cry3. We propose to investigate this effect of green light on greening and photosynthetic capacity during seedling establishment in light. Genome-wide expression, DNA-binding and protein-interaction analysis will enable us to interrogate the potential function of cry3 as a green light sensor. Finally, we will combine the gained knowledge in a computational model, to predict how green light sensing via cry3 affects adult plant performance in different light environments. With this project, we fill the knowledge gap of how plants detect and process green light. Importantly, we address a completely new role for chloroplasts as environmental (light) signaling hubs, which will foster other studies to organelle-specific sensors and signaling processes. Lastly, the ability to actively adapt photosynthetic capacity via light signaling pathways opens doors for crop improvement in sub-optimal and artificial light environments.

Plants grow in interaction with microbes in order to survive. These microbes can enter the next plant generation of the plant via the seed. The main research questions of this project are 1) to determine whether plant genetics and seed characteristics affect the recruitment of microbes, 2) to identity microbes that contribute to seed and plant performance in drought stress and 3) to understand the mechanisms underlying these beneficial plant-microbe interactions. Overall, this research contributes to improving seed and plant performance in a changing environment.