Engineering the auxin-inducible degron system for tunable in vivo control of organismal physiology

The auxin-inducible degron (AID) system is designed for the rapid and near-complete degradation of a specific target protein in vivo. However, to understand the dynamics of complex physiological networks, researchers often need methods that produce graded, quantitative changes in degradation rates for multiple proteins simultaneously. Here, we develop the AID system for in vivo, quantitative control over the abundance of multiple proteins simultaneously. First, by measuring and modeling the on- and off-target activities of different AID system variants in Caenorhabditis elegans, we characterize a variant of the E3 ubiquitin ligase subunit TIR1, which provides improved degradation activity compared to the original AID and AID2 systems. Then, we develop a TIR1 expression construct that enables simultaneous pan-somatic and germline protein degradation. Finally, we expand the AID toolkit to allow independent, simultaneous degradation of two distinct tissue-specific proteins. Together, these technologies enable new in vivo approaches for studying quantitative cellular biology and organismal dynamics.