Architecture of a peptidoglycan peptidase complex involved in morphological transition in Helicobacter pylori

ABSTRACT Peptidoglycan is a meshwork macromolecule, made of polysaccharide strands cross-linked by short peptides, which encases the cytoplasmic membrane of bacteria and protects them against turgor pressure. Peptidoglycan peptidases are membrane or periplasmic enzymes that cleave these peptides, either lowering the cross-linking level of peptidoglycan to sculpt bacterial shape or allowing cell elongation by making space for the insertion of neosynthesized glycan strands. In the pathogen Helicobacter pylori , shape is important for virulence, and transition to a coccoid form after prolonged growth enables immune evasion. One particular endopeptidase, HdpA, is known to be involved in the maintenance of cell shape and in the transition to coccoids. Here we show that along growth, HdpA is constantly associated with LhiA, an inner membrane chaperone lipoprotein that keeps it in check while protecting it from fast proteolysis. The crystal structure of the HdpA-LhiA complex suggests that this interaction freezes the autoinhibitory interaction between the first domain of HdpA and the third, catalytic domain. Analysis of the evolution of the HdpA and LhiA protein levels over growth suggests that transition to coccoids is not triggered by a burst in HdpA activity but rather by a gradual weakening of the sacculus caused by the small fraction of free HdpA in equilibrium with LhiA-sequestered HdpA. SIGNIFICANCE STATEMENT The cell wall, the exoskeleton of bacteria, is the target of numerous antibiotics. Its principal component, peptidoglycan, is remodeled by an interplay between peptidoglycan synthases and hydrolases to accomodate bacterial growth. Because their activity can be harmful, hydrolases have to be tightly regulated. We discovered the dedicated inhibitory chaperone of a H. pylori peptidoglycan hydrolase and showed how the chaperone keeps the hydrolase in check in the cytoplasmic membrane and releases it slowly to allow it to perform its task, ultimately triggering a shape transition to a spherical form important for immune evasion. The crystal structure of the complex gives clues to the mechanism of peptidase activation, suggesting strategies to design agonists that could be used as antibacterials.