A lipid fenestration-gated membrane depolarization mechanism expands the repertoire of CRISPR-mediated anti-phage defense strategies

Prokaryotic Type III CRISPR-Cas systems synthesize cyclic oligoadenylate (cOA) second messengers that activate CRISPR-associated Rossmann fold (CARF) immune effectors during viral infection. Here we characterize Chp1, a membrane-embedded CARF effector that assembles as a tetrameric pore harboring autoinhibitory lipid fenestrations that occlude the pore in the inactive state. cOA binding triggers a structural rearrangement that (i) closes the fenestrations, (ii) eliminates the lipid obstruction of the pore to open it, and (iii) remodels the pore entrance from hydrophobic to polar to allow ion permeation. This conformational switch triggers depolarization of the membrane of the infected cell, which enters growth arrest and becomes inhospitable for viral replication. Our results uncover a lipid-gated mechanism that expands the repertoire of CRISPR-mediated defense strategies.