Minute-scale control of ubiquitin-mediated degradation reveals dynamics of bacterial secreted effector-functions

Precise temporal control of protein abundance is essential for dissecting dynamic cellular processes. While degron-based systems enable rapid protein depletion in eukaryotic cells, comparable tools are lacking for bacterial effectors delivered into host cells during infection. Here, we establish AIDE (Auxin-Inducible Degradation of Effectors), a host-directed degradation platform that harnesses the ubiquitin-proteasome system to selectively eliminate secreted bacterial proteins, including membrane-integrated effectors. By integrating a minimal auxin-inducible degron (AID) tag into effector genes, AIDE enables rapid, reversible, and spatially confined degradation while preserving native expression and secretion. We apply AIDE to Chlamydia trachomatis and show, that the membrane-integrated deubiquitinase Cdu1 suppresses autophagy early and later promotes developmental transitions, whereas the integral membrane fusogen IncA remains continuously required to maintain homotypic inclusion fusion. This AIDE platform provides minute-scale, spatiotemporal control over bacterial effector activity and offers a broadly applicable framework for dissecting virulence mechanisms and host-pathogen interactions across diverse secretion-dependent pathogens.