Structural basis for phage single gene lysis protein mechanisms

The rapid emergence of antibiotic resistant bacterial strains represents a significant threat to public health, making the development of novel therapeutic strategies critical. Bacterial cell wall biosynthesis has been exploited as a major target for antibiotics and historically been quite successful in treating bacterial infections. A major component of the bacterial cell wall is the peptidoglycan (PG) layer, providing structural support to maintain cell shape and protect bacteria from osmotic lysis. One promising strategy to inhibit PG biosynthesis is to leverage the naturally occurring bacteriophage-derived lysis proteins. Small lytic phages of the families Microviridae and Leviviridae disrupt the formation of the PG matrix through a single gene lysis protein (Sgl). Sgls lack enzymatic activity to degrade cell wall directly and instead induce the host cell to undergo autolysis by inhibiting cell wall synthesis. Three Sgls have been identified that target PG biosynthesis enzymes and act as protein antibiotics. The A2 protein of levivirus Qβ, protein E of ΦX174 (EΦX174) and lysis protein of levivirus M (LysM) were shown to inhibit MurA, MraY and MurJ steps of the PG synthesis pathway respectively. To date, the molecular details of how Sgls inhibit PG biosynthesis enzymes are not well understood. Here we present the cryo-EM structure of the EΦX174-MraY inhibition complex which reveals that E inhibits MraY activity by blocking the substrate binding sites. Furthermore, we are currently exploring other peptidoglycan targeting Sgls from various bacteriophages to expand our understanding of cell wall synthesis inhibition by protein antibiotics. Structure elucidation of these Sgl-PG biosynthetic enzyme complexes helps identify structural properties of the inhibitor binding sites, providing insights into rational design strategies for developing novel bacteriophage Sgl-based inhibitors targeting cell wall biosynthesis.