UC Berkeley

The innate immune system of mammals encodes several families of immune detector proteins that monitor the cytosol for signs of pathogen invasion. One important but poorly understood family of cytosolic immunosurveillance proteins is the NLR (nucleotide binding domain, leucine-rich repeat containing) proteins. Work presented here demonstrates that one subfamily of NLRs, the NAIPs (NLR family, Apoptosis Inhibitory Proteins), are activated by specific interaction with bacterial ligands, such as flagellin. NAIP activation leads to assembly of a large multiprotein complex called the inflammasome, which initiates innate immune responses by activation of the Caspase-1 protease. NAIPs therefore appear to detect pathogen molecules via a simple and direct receptor-ligand mechanism. Interestingly, other NLR family members appear to detect pathogens indirectly, perhaps by responding to host cell `stress' caused by the pathogen. Thus, the NLR family may have evolved surprisingly diverse mechanisms for detecting pathogens.

Susceptibility to the intracellular bacterial pathogen Legionella pneumophila was mapped to a discrete genetic locus in the mouse containing multiple tandem gene paralogues constituting the NAIP gene array over ten years ago, but functional understanding of the NAIP array, and in particular whether different genes in the array perform diverse or redundant functions in host defense remains enigmatic. Here we show that NAIP proteins monitor the cytoplasm of host innate immune cells for the presence of bacterial flagellin, and the inner-rod proteins of bacterial type III secretion systems. Specific interaction of NAIP5 and NAIP6 with bacterial flagellin, and NAIP2 with inner-rod proteins (from a variety of pathogenic bacteria) promotes inflammasome assembly and activation. The `orphan' receptor NAIP1 appears to detect a narrow subset of inner-rod proteins, but the structural basis for this selectivity and its functional importance are unknown.

Finally, we have mapped the ligand-specificity determining region of the NAIPs to a ~200 amino acid region of the LRR domain that spans seven structural repeats that exhibit a high degree of polymorphism among the NAIP paralogues. Whether the region is sufficient for binding specific ligands is an open question. We have used structural modeling and polymorphism mapping of the NAIP LRR domains to identify putative ligand-binding residues that may be under selective pressure from bacterial pathogens. Thus, the NAIP gene array has evolved to recognize functionally constrained molecules of pathogenic bacteria, and represents an exquisite mechanism of host defense.