Antimicrobial-resistance plasmids encode Evangelion, a widespread DUF4062 anti-phage defence family

Abstract

Mobile genetic elements have profoundly shaped the evolution of bacterial anti-phage immunity, yet much of this defence repertoire remains undiscovered. Antimicrobial-resistance plasmids are well known for disseminating antibiotic-resistance genes, but whether they also serve as reservoirs of previously unrecognised antiviral immunity remains poorly understood. Here, we identify Evangelion, a widespread family of single-gene anti-phage defence systems, through phenotype-guided interrogation of a naturally occurring methicillin-resistant Staphylococcus aureus plasmid. Eva01, the founding member of the family, protects against lytic Silviavirus phages and is built around a conserved DUF4062 core coupled to a highly diversified auxiliary region that is essential for defence activity. Evangelion systems are enriched on antimicrobial-resistance plasmids but are distributed across diverse bacterial hosts and mobile genetic elements, revealing an evolutionarily conserved defence framework that has diversified through horizontal gene transfer and adaptation to distinct phage environments. Genetic, structural and functional analyses support a model in which Eva01 senses intracellular phage replication-associated processes and couples activation of a DUF4062 effector to NAD depletion and abortive infection. Together, our findings define a previously unrecognised family of mobile anti-phage defence systems, establish DUF4062 proteins as a new component of the bacterial anti-phage repertoire, and demonstrate that phenotype-guided interrogation of mobile genetic elements provides a powerful strategy for discovering defence systems beyond the reach of current computational approaches.