The phage anti-restriction induced system: new insights into bacterial immunity and bacteriophage escape strategies

Two recent publications in Nature reveal the detailed structural mechanisms underlying the recognition of infection by the bacterial Phage Anti-Restriction Induced System (PARIS). 1,2These findings are important as they show a new strategy for the recognition of viral infections, shed light on principles of host-virus co-evolution and might pave the way for the development of new antimicrobial strategies.PARIS belongs to the toxin-antitoxin (TA) systems, which are small genetic elements that are involved in a plethora of bacterial functions, including plasmid maintenance, biofilm production, persistence, virulence and defense against bacteriophages.They are common in nearly all prokaryotic phyla and >200,000 putative TA modules have been identified today across 41,610 analyzed genomic assemblies. 3Among the different classes, type II TA systems, in which an antitoxin protein binds and inhibits the toxin protein, are best characterized.The PARIS system constitutes a bacterial defense mechanism consisting of an ABC ATPase protein (AriA) and a TOPRIM/OLD-family nuclease (AriB).However, the molecular mechanisms of how PARIS inhibits bacteriophage propagation and how phages can escape PARIS immunity remained unclear.Using cryo-EM structures with resolution down to 3.1 , the authors show that the antitoxin AriA forms a stable homohexameric ring structure that can tightly bind and sequester up to three units of the AriB toxin, effectively inhibiting its nuclease activity.Upon infection, bacteria use restriction-modification (RM) and CRISPR/Cas systems to cleave foreign DNA thereby blocking phage propagation.To escape this "first-line" defense mechanism, bacteriophages can express factors that counter host defenses.In the case of T7, the phage-encoded protein Ocr ('overcome classical restriction') can bind the restriction complex and inhibit its recognition of phage DNA.Notably, PARIS not only recognizes T7-encoded Ocr but also T4-encoded structurally dissimilar antirestriction protein Arn25.The ability to identify such diverse viral inhibitors of restriction defense mechanisms is likely due to electrostatic interactions between positively charged residues at AriA and negatively charged surfaces on Ocr and Arn25.The new cryo-EM data indicate that upon recognition of Ocr, AriA undergoes a conformational change that decreases its affinity for AriB, which results in its release from the AriA-AriB complex.Subsequently, AriB dimerizes into homodimers, which significantly enhances its nuclear activity.The authors demonstrate that, once activated, AriB triggers abortive infection by blocking bacterial translation.Specifically, AriB cleaves bacterial lysine tRNA (tRNA Lys ), thereby blocking both bacterial growth and phage replication.This