Comparative analysis and directed protein evolution yield an improved degron technology with minimal basal degradation, rapid inducible depletion, and faster recovery of target proteins.

Biological mechanisms are inherently dynamic, requiring precise and rapid gene manipulation for effective characterization. Traditional genetic perturbation tools such as siRNA and CRISPR knockout operate on timescales that render them unsuitable for exploring dynamic processes or studying essential genes, where chronic depletion can lead to cell death. Here, we compared four major inducible degron systems-dTAG, HaloPROTAC, and two auxin-inducible degron (AID) tools-in human pluripotent stem cells. We evaluated basal degradation levels, inducible degradation kinetics, and recovery dynamics for endogenously tagged genes. While the AID 2.0 system is the most efficient for rapid protein degradation, it exhibited higher basal degradation and slower recovery after ligand washout. To address these challenges, we applied directed protein evolution, incorporating base-editing-mediated mutagenesis and iterative functional selection and screening. We discovered novel OsTIR1 variants, including S210A, with significantly enhanced overall degron efficiency. The resulting system, designated as AID 3.0, demonstrates minimal basal degradation and rapid and effective target protein depletion and substantially rescues the cellular and molecular phenotypes due to basal degradation or slow target protein recovery in previous systems. We conclude that AID 3.0 represents a superior degron technology, offering a valuable tool for studying gene functions in dynamic biological contexts and exploring therapeutic applications. Additionally, the research strategy used here could be broadly applicable for improving other degron and biological tools.