The Yersinia pestis virulence effector YopM binds to a key regulatory site on the human pyrin death domain to inhibit inflammasome activation and effector-triggered immunity

Abstract

Bacteria in the genus Yersinia use a type III secretion system to inject several effectors into host cells to disrupt multiple signaling processes. Two effectors disrupt host signaling by inactivating RhoA GTPases. Inactivation of RhoA triggers pyrin inflammasome assembly in infected phagocytes leading to a protective immune response. A third protein, YopM, is an essential virulence factor that counteracts effector-triggered immunity by inactivating pyrin. YopM has a leucine-rich repeat (LRR) domain and hijacks host kinases to inactivate pyrin by phosphorylation. Previously, the LRR domain of Yersinia pestis YopM was implicated in binding to an N-terminal region of human pyrin, which includes the eponymous pyrin domain (PYD), a member of the death domain family. However, the interaction mechanism was undefined. Using a bacterial two-hybrid assay, protein biochemistry and X-ray crystallography, we determined that the concave surface of the YopM LRR domain binds to the PYD. Identification of critical residues in the interaction revealed that YopM binds PYD R42, an amino acid important for positive and negative regulation of pyrin. YopM binding to the PYD was reduced by R42W, a codon change associated with the autoinflammatory disease Familial Mediterranean Fever (FMF). Furthermore, we show that YopM codon substitution variants defective for PYD binding fail to inhibit the pyrin inflammasome in human monocytes infected with Yersinia. In addition, we found that PYD binding is dispensable for YopM to inhibit the inflammasome in murine macrophages, suggesting this effector uses a distinct mechanism to target mouse pyrin. These results define how Y. pestis YopM binds the human PYD and provide insights into how this interaction likely selected for pyrin gain of function variants resulting in FMF. SIGNIFICANCEPyrin is an inflammasome sensor encoded by the MEFV gene that is notable for its role in the autoinflammatory disease Familial Mediterranean Fever (FMF) and immunity to the plague agent Yersinia pestis. Y. pestis normally prevents inflammasome activation using the virulence factor YopM which binds pyrin and inhibits effector-triggered immunity. Gain of function mutations in MEFV that cause FMF were likely selected during historic plague pandemics to counteract YopM. Here, we defined the molecular mechanism of the YopM-pyrin interaction, which revealed that the effector binds to a key site of positive and negative regulation on the N-terminal death domain. These findings have important implications for understanding how YopM promotes pathogenesis and likely selected for gain of function mutations in MEFV.