Elucidating the antibiotic sensing mechanism of VanB vancomycin‐resistant Enterococci

Abstract

The antibiotic vancomycin is used as a last resort to treat persistent infections caused by Gram‐positive pathogens. Vancomycin kills bacteria by binding a peptidoglycan precursor, thereby inhibiting cell‐wall biosynthesis. An alarming type of resistance to this antibiotic comes in the form of vancomycin‐resistant Enterococci(VRE). VRE have acquired genes that allow them to remodel the cell‐wall precursor and prevent vancomycin binding. Expression of these remodeling genes is under control of the VanSR two‐component system. VanS is a membrane‐bound sensor kinase that recognizes the vancomycin signal, and in response activates the transcription factor VanR, which activates expression of the remodeling genes. However, very little is known about how VanS senses the antibiotic.To date, nine different types of VRE have been discovered, with VanA and VanB types responsible for the vast majority of human infections. Since vancomycin can induce the expression of both VanA and VanB resistance genes, we hypothesize that the VanS proteins from these types are activated by directly binding to vancomycin. We used in vitro autokinase assays to show that vancomycin directly activates VanS from VanB VRE (VanSB), while having no direct effect on VanSA­. We isolated the VanSB periplasmic sensor domain and used fluorescence anisotropy to show that it directly binds to a fluorescent vancomycin analog. Computational modeling predicts that the VanSB sensor domain adopts a PAS‐like fold, and HDX‐MS experiments supported this prediction and identified a potential vancomycin‐binding site. We also developed vancomycin photoprobes to confirm this binding site and to elucidate vancomycin’s orientation in the interaction. These results demonstrate how VanSBcan directly sense vancomycin in the environment to activate the resistance mechanism in VanB VRE, providing a promising therapeutic target to combat these dangerous pathogens.