DipM controls multiple autolysins and mediates two regulatory feedback loops promoting cell constriction in C. crescentus

Abstract

Proteins containing a catalytically inactive LytM-type endopeptidase domain have emerged as important regulators of cell wall-degrading enzymes in bacteria. Although these so-called LytM factors are wide-spread among species, the range of functions they fulfill and their precise modes of action are still incompletely understood. In this work, we study the LytM factor DipM, a protein required for proper cell division in the model species C. crescentus. We show that the LytM domain of DipM interacts directly with multiple autolysins, including the lytic transglycosylases SdpA and SdpB, the amidase AmiC and the putative carboxypeptidase CrbA, and stimulates the activities of SdpA and AmiC. The crystal structure of the LytM domain of DipM reveals conserved features, including a distinctive groove. Modeling studies suggest that this groove could represent the docking site of AmiC. The architecture of the binding interface in the DipM-AmiC complex is very similar to that observed for the LytM domain of EnvC in complex with its autoinhibitory restraining arm, suggesting a conserved role of the groove in the interaction of LytM factors with their (auto-)regulatory targets. In line with this hypothesis, a mutation in the groove abolishes DipM function. Interestingly, single-molecule tracking studies reveal that the recruitment of DipM and its regulatory targets SdpA and SdpB to the division site is mutually interdependent, with DipM establishing a self-reinforcing cycle that gradually increases lytic transglycosylase activity at the cell center as division progresses. At the same time, the DipM-dependent activation of AmiC leads to the production of denuded peptidoglycan, generating a spatial cue that attracts FtsN to the division site and thus, in turn, again promotes the recruitment of DipM. Collectively, these findings show that DipM is a central regulator that acts at the intersection of different peptidoglycan remodeling pathways and coordinates the activities of various classes of autolysins to promote cell constriction and daughter cell separation.