A family of endonucleases blocks nanotube-mediated plasmid exchange.

Horizontal transfer of small non-conjugative plasmids is primarily attributed to transformation, transduction or comobilization with conjugative elements; however, transfer through intercellular membranous nanotube conduits can also occur. Here we show that nanotube-dependent plasmid exchange (NPex) operates bidirectionally between bacteria, enabling plasmid donation and, to a lesser extent, plasmid acquisition. We identified a Bacillus subtilis isolate, BSB1, deficient in NPex and show that a prophage-encoded factor, YokF, blocks plasmid transmission. YokF is an endonuclease that localizes to the membrane of donor bacteria, where it interacts with the nanotube component, FlhA, to impede plasmid transfer through DNA degradation. We further show that YokF provides an advantage to donor bacteria by restricting the sharing of beneficial plasmids with competing neighbouring cells. Bioinformatics and functional analyses revealed that YokF homologues are widespread across Gram-positive bacteria, representing a conserved family of gatekeepers that restrict plasmid flow via NPex.