Phase-variable restriction modification systems dynamically regulate plasmid transmission in Neisseria gonorrhoeae

Horizontal gene transfer (HGT) in bacteria is shaped by restriction-modification systems (RMSs) that define genetic barriers between species and lineages. Neisseria gonorrhoeae harbours numerous RMS, most of which are part of its core genome. Here, we show that phase variation in these RMSs can limit interspecies and intraspecies plasmid exchange. While NlaIV likely influenced the acquisition of pConj from the meningococcus, phase variation of the NgoAV RMS produces epigenetically heterogeneous populations that present variable bottlenecks to within-species plasmid transmission, influencing the spread of anti-microbial-resistance plasmids, pConj and pbla. A LEAT sequence extends or retracts a molecular ruler within the HsdS specificity subunit, altering spacing of recognition motifs, while truncation of the protein leads to a switch from non-palindromic to palindromic recognition motifs. Thus, while the repertoire of gonococcal RMSs is largely conserved, phase-variation dynamically modulates gene flow, shaping plasmid transmission, and the evolution and spread of antimicrobial resistance.