An engineered streptavidin condensate platform for chemically inducible control of endogenous proteins in mammalian cells

Abstract

Inducible control of protein activity with temporal precision is essential for understanding and engineering dynamic cellular behaviors. However, current inducible molecular tools largely rely on overexpression of target proteins, which often disrupts the signaling pathways and cellular functions under investigation. A generalizable method to achieve inducible control of endogenous proteins in mammalian cells remains an unmet need. Here, we present a versatile platform based on engineered streptavidin biomolecular condensates to trap and release endogenously tagged proteins. By tagging endogenous loci with a short streptavidin-binding peptide via CRISPR knock-in, our synthetic streptavidin condensates efficiently partition and functionally inhibit the tagged endogenous proteins. The sequestered cargo protein is rapidly released upon the addition of biotin, restoring protein activity within minutes. We demonstrated the broad applicability of this system by controlling diverse endogenous targets: the anterograde motor KIF5B and retrograde motor DYNC1H1, which regulate intracellular vesicle trafficking, and the Arp2/3 complex subunit ARPC3, which regulates actin dynamics. Furthermore, we developed a dual-inducible system based on rapamycin-dependent condensation of streptavidin, enabling both rapid sequestration and release of endogenous proteins at user-defined time points. Altogether, this engineered streptavidin condensate platform provides a robust, rapid, and scalable approach for manipulating endogenous protein function under physiologically relevant conditions in both basic and translational research.