Structures and functions of the inflammasome engine

Abstract

Inflammasomes are molecular machines that carry out inflammatory responses on challenges by pathogens and endogenous dangers. Dysregulation of inflammasome assembly and regulation is associated with numerous human diseases from autoimmunity to cancer. In recent years, significant advances have been made in understanding the mechanism of inflammasome signaling using structural approaches. Here, we review inflammasomes formed by the NLRP1, NLRP3, and NLRC4 sensors, which are well characterized structurally, and discuss the structural and functional diversity among them.

Keywords: IL-1; Inflammasome; NLRC4; NLRP1; NLRP3; caspase-1; pyroptosis.

FIG 1.

The NAIP-NLRC4, NLRP3, and NLRP1 inflammasome pathways. Gram-negative bacteria can use the type III secretion system to release various products into the cytosol, which are detected by NAIPs to seed the NLRC4 inflammasome. Broader insults to the cell that convergently result in K⁺ efflux activate NLRP3, which binds NEK7 to assemble the NLRP3 inflammasome. NLRP1 undergoes autoproteolysis within the FIIND, leaving noncovalently associated NT domain and the CT UPA-CARD. Bacterial and viral products directly proteolyze or ubiquitinate the NT domain to promote functional proteasomal degradation to liberate the active UPA-CARD. NLRP1 is further regulated by DPP9 and its small-molecule inhibitor VbP. All inflammasomes incorporate pro–caspase-1, either directly or through the adaptor protein ASC, which results in proximity-driven activation of caspase-1. Active caspase-1 cleaves pro–IL-1β into mature IL-1β and FL-GSDMD into NT and CT fragments. GSDMD-NT binds to acidic lipids, oligomerizes, and inserts into the membrane to form the GSDMD pore through which IL-1β is secreted. The GSDMD pore can also increase permeability of the membrane to various ions and water, which can ultimately result in osmotic swelling and pyroptosis. NT, N-terminal; MAC, membrane attack complex.

FIG 2.

Structural insights on NAIP-NLRC4 inflammasomes. A, Domain architectures and protein-protein interactions. B, Activated NLRC4 forms disk-like oligomers, which are assembled by NACHT(NLRC4)-NACHT(NLRC4) and LRR(NLRC4)-LRR(NLRC4) interactions. C, Top, NLRC4 in an autoinhibited state. Bottom, rotation of the NBD and HD1 relative to the rest of the protein required for activation of NLRC4. D, Left, Structure of NAIP5 bound to Salmonella flagellin FliC. Right, Legionella flagellin FlaA binds to NAIP5 and pries NAIP5 into an active conformation, exposing surfaces to propagate the oligomerization of NLRC4. The CT helix of flagellin binds to a deep pocket in NAIP5. BIR, Baculovirus inhibitor of apoptosis repeat; ID, insertion domain.

FIG 3.

Structural insights on the NLRP3 inflammasome. A, Domain architectures and protein-protein interactions among them for the inflammasome assembly. B, Left, NLRP3 bound with NEK7. Domains are color coded as in Fig 3, A. Middle, Modeled active conformation of NLRP3 based on NLRC4 may be required for proposed oligomerization of NLRP3. Right, Once activated, oligomerization of the NLRP3-NEK7 complex is propagated by NACHT(NLRP3)-NACHT(NLRP3) and NEK7-LRR(NLRP3) interactions to form full disk-like oligomers. C, Left, Crystal structure of NEK7 (C-lobe only) bound to NEK9. Right, NEK9 interacts with NEK7 at the surface where NLRP3 interacts, making NEK7-NLRP3 and NEK7-NEK9 interactions mutually exclusive.

FIG 4.

Structural insights on the NLRP1 inflammasome. A, Domain architecture of NLRP1. Interactions of NLRP1 with DPP9 are shown with lines. B, Cryo-EM structure of the NLRP1-DPP9 ternary complex, composed of NLRP1^FL-FIIND, NLRP1^CT-UPA, and DPP9. NLRP1^CT-UPA N-terminal peptide interacts with DPP9 by inserting itself in the DPP9 active-site tunnel. The UPA^FL-UPA^CT interaction interface is marked. Domains are color coded as in Fig 4, A. C, Cryo-EM structure of NLRP1-DPP9 bound with VbP. VbP interacts with the active-site tunnel residues of DPP9 and displaces NLRP1^CT-UPA.

FIG 5.

Structural insights on filamentous assemblies in inflammasomes. A, Polymerization of ASC PYDs forms a helical filament. B, Polymerization of ASC CARDs forms a helical filament. C, Domain architecture of cleaved CT fragment of CARD8 and NLRP1. Oligomerization of CARD is facilitated by UPA-UPA interactions. D, UPA-UPA filament modeled by UPA-UPA dimer observed in the NLRP1-DPP9 ternary complex (PDB ID 6X6A). E, Schematic diagram of how UPA oligomerization facilitates CARD filament formation. F, A variant of CARD filament formed by NLRP1 CARD dimers that is about twice the thickness of a conventional CARD filament.