Understanding and Engineering Chemically Activated Ubiquitin Ligases - Project Summary/Abstract The objectives of my research program are to understand and engineer protein degradation by the ubiquitin-proteasome system—a critical signaling mechanisms that all animals, plants, and fungi use to perceive and adapt to their environment. The ubiquitin-proteasome system acts like the recycling system of the cell, where specific proteins are marked for recycling by ubiquitin and are cut into peptides by the proteasome to be further broken down and made into new proteins. The ability of the ubiquitin-proteasome pathway to remodel a cell’s proteome in a rapid and specific way has perhaps led to its ubiquity throughout the evolution of eukaryotes. The strong conservation of ubiquitin in eukaryotes also makes it a prime candidate for engineering control systems in biology. The ubiquitin- proteasome machinery in humans is frequently implicated in cancers, neurodegenerative diseases, and metabolic disorders among other diseases, due to it is involvement in cell cycle regulation, vascular development, and inflammation, among other critical processes. By improving our understanding of how the ubiquitin-proteasome pathway functions or fails to function, we may uncover new ways to treat or prevent human disease. The ubiquitin-proteasome pathway plays perhaps an even more central role in plants where it is involved in nearly all known plant hormone signaling pathways to coordinate their growth and respond to changes in their environment, including stresses such as pests and pathogens. These chemical hormones activate ubiquitin ligases which trigger degradation of repressive transcription factors leading to activation of hormone-responsive gene transcription. Interestingly, animals and microbes also perceive plant hormones which have wide ranging effects on their physiology. Animals and microbes also produce plant hormones or similar molecules to aberrantly activate ubiquitin-proteasome signaling and manipulate plants for their benefit. Our research aims to understand the molecular mechanism of how information is transferred through these ubiquitin-proteasome signaling pathways and how these hormone-signaling and biosynthesis pathways have coevolved in plants and other eukaryotes. To do this we will use a deep mutational scanning approach enabled by a massively parallel functional assays using a biosensor we recently developed. In parallel, we aim to re-engineer these chemically activated ubiquitin ligases to detect related and potentially novel chemical compounds and to act as rapid metabolic controllers. These molecular tools will improve our ability to control and engineer biological systems and sustainably biomanufacture these plant hormones and related chemicals, including important agricultural and industrial chemicals, nutritional supplements, and pharmaceuticals.
