Defects in normal autophagic pathways are implicated in numerous human diseases-such as neurodegenerative diseases, cancer, and cardiomyopathy-highlighting the importance of autophagy and its proper regulation. Herein we show that Vibrio parahaemolyticus uses the type III effector VopQ (Vibrio outer protein Q) to alter autophagic flux by manipulating the partitioning of small molecules and ions in the lysosome. This effector binds to the conserved V o domain of the vacuolar-type H + -ATPase and causes deacidification of the lysosomes within minutes of entering the host cell. VopQ forms a gated channel ∼18 Å in diameter that facilitates outward flux of ions across lipid bilayers. The electrostatic interactions of this type 3 secretion system effector with target membranes dictate its preference for host vacuolar-type H + -ATPase-containing membranes, indicating that its pore-forming activity is specific and not promiscuous. As seen with other effectors, VopQ is exploiting a eukaryotic mechanism, in this case manipulating lysosomal homeostasis and autophagic flux through transmembrane permeation.utophagy is a cellular process by which cells degrade and recycle cytoplasmic contents by encapsulating them within a distinctive double bilayer membrane vesicle for delivery to the degradative lysosome (1). Disruption of normal autophagic pathways is implicated in numerous human diseases, stressing the importance of autophagy and its proper regulation (2). Vibrio parahaemolyticus, a Gram-negative marine bacterium and a major cause of gastroenteritis due to the consumption of contaminated raw or undercooked seafood, induces autophagy during infection (3). V. parahaemolyticus harbors two type 3 secretion systems (T3SSs), molecular syringes that enable the translocation of bacterial proteins, known as effectors, into the eukaryotic host (3). The first T3SS (T3SS1) orchestrates a temporally regulated cell death mediated by the induction of autophagy, followed by cell rounding and resulting in lysis of the host cell (4). T3SS1 effector VopQ, also known as VepA (vp1680), is both necessary and sufficient for the rapid induction of autophagy, even in the presence of known chemical inhibitors of autophagy (5).VopQ is a 53-kDa protein with no apparent homology to any proteins outside of the Vibrio species. Vibrio homologs of VopQ have no known function or conserved structural domain. Previous work from our laboratory has shown that VopQ is a cytotoxic effector that accelerates host cell death and is essential in protecting V. parahaemolyticus from phagocytic uptake during infection (5). Based on microbial genetic studies, VopQ was shown to be necessary for the formation of an extensive network of autophagic vesicles in host cells within an hour of V. parahaemolyticus infection (5). Strikingly, recombinant VopQ alone is sufficient to induce this massive accumulation of autophagic vesicles, observed within minutes of microinjection of recombinant VopQ (picomolar concentrations) into eukaryotic cells (5). A recent report shows that Vo...