A possible mechanism of Ub-mediated autophagic sequestration of invading bacteria and transfection reagent–coated latex beads. After internalization and endosomal rupture, Ub is conjugated to host cellular proteins in endosomes that contain Salmonella or transfection reagent–coated latex beads (top). Ub would be recognized by three pivotal components of the autophagic machinery, notably the Atg16L1 complex, the ULK1 complex, and Atg9L1 (bottom right). Atg16L1 localizes to the ubiquitinated target through three mechanisms, the interaction of coiled-coil domain (CCD) with FIP200, the interaction of WD repeats (WDR) with Ub, and the 194–195 region-mediated mechanism (bottom left).