Control of protein degradation and transcriptional dynamics in the auxin response

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Coordinating the timing of responses both within and between cells is critical for multicellular behaviors like development. One way to evolve (or engineer) a molecular pacer is via induced turnover of transcriptional repressors acting at multiple loci—a solution observed in diverse eukaryotes. Yet we know remarkably little about how protein degradation kinetics translate into downstream transcriptional responses that lead to outcomes like changes in cell fate. One possible reason is the lack of available models for high-resolution structure-function analysis of degradation-linked transcriptional activation. We have leveraged the auxin response, at the heart of nearly every aspect of plant biology, as a model to investigate general principles underlying ubiquitin-mediated degradation and its connection to transcriptional activation and morphogenesis. The small-molecule triggered degradation in the auxin pathway offers a unique advantage for these studies, and has facilitated our engineering of auxin-induced degradation and transcriptional activation in yeast. Our extensive work with our ‘AuxInYeast’ system has led to a central hypothesis: the auxin system functions as a developmental timer in plants, and similar logic circuits act in many eukaryotes. One recent insight into the molecular mechanism underlying the auxin timer was our discovery that transcriptional repression in the auxin circuit, conferred by a Groucho/Tup1/TLE-type corepressor called TPL, requires interaction with the Mediator complex. Our results suggest a new model of transcriptional regulation where corepressors can stabilize the Pre-Initiation Complex in the absence of RNA Polymerase II, priming loci for rapid activation. In addition, we have shown in transgenic plants that the rate of degradation-triggered removal of the TPL corepressor sets the pace of de novo organogenesis in the root. Here, we will rigorously test the emergent model that corepressor- based priming facilitates coordination of rapid transcriptional bursts at multiple loci across the genome, and facilitates cell-cell synchrony during morphogenesis. Specific research projects will: (1) Deliver a high spatiotemporal resolution, integrated, functional map of a single synthetic yeast locus transitioning from repressed to active state, including composition/placement of protein complexes and chromatin modifications; (2) Dissect the mechanism of a novel autonomous TPL repression domain we have identified that is found in thousands of proteins, and quantify the impacts on repressive function of cancer-associated variants in select proteins; (3) Build an in vivo cell fate tracker to probe the connection between synchrony in transcription and morphogenesis. Together, the proposed work will provide a mechanistic framework for degradation-initiated transcriptional activation in the auxin response, and potentially provide insights into fundamental properties in common with many corepressor-primed systems. These insights can inform our understanding of degradation- and transcription-associated human disease, as well as guiding future design of synthetic circuits using auxin components for therapeutic applications.