A distinct inhibitory mechanism of the V-ATPase by Vibrio VopQ revealed by cryo-EM

The Vibrioparahaemolyticus T3SS effector VopQ targets host-cell V-ATPase, resulting in blockage of autophagic flux and neutralization of acidic compartments. Here, we report the cryo-EM structure of VopQ bound to the V-o subcomplex of the V-ATPase. VopQ inserts into membranes and forms an unconventional pore while binding directly to subunit c of the V-ATPase membrane-embedded subcomplex V-o. We show that VopQ arrests yeast growth in vivo by targeting the immature V-o subcomplex in the endoplasmic reticulum (ER), thus providing insight into the observation that VopQ kills cells in the absence of a functional V-ATPase. VopQ is a bacterial effector that has been discovered to inhibit a host-membrane megadalton complex by coincidentally binding its target, inserting into a membrane and disrupting membrane potential. Collectively, our results reveal a mechanism by which bacterial effectors modulate host cell biology and provide an invaluable tool for future studies on V-ATPase-mediated membrane fusion and autophagy. Cryo-EM visualization of the bacterial pore-forming toxin VopQ bound to its host V-ATPase membrane-domain target reveals how cytotoxic effector proteins promote membrane disruption and inhibit ATPase function.