The NLR family of innate immune and cell death sensors

Abstract

Nucleotide-binding oligomerization domain (NOD)-like receptors, also known as nucleotide-binding leucine-rich repeat receptors (NLRs), are a family of cytosolic pattern recognition receptors that detect a wide variety of pathogenic and sterile triggers. Activation of specific NLRs initiates pro- or anti-inflammatory signaling cascades and the formation of inflammasomes-multi-protein complexes that induce caspase-1 activation to drive inflammatory cytokine maturation and lytic cell death, pyroptosis. Certain NLRs and inflammasomes act as integral components of larger cell death complexes-PANoptosomes-driving another form of lytic cell death, PANoptosis. Here, we review the current understanding of the evolution, structure, and function of NLRs in health and disease. We discuss the concept of NLR networks and their roles in driving cell death and immunity. An improved mechanistic understanding of NLRs may provide therapeutic strategies applicable across infectious and inflammatory diseases and in cancer.

Keywords: DAMP; IL-18; IL-1β; NF-κB; NLR; NLR network; PAMP; PANoptosis; PANoptosome; RIPK; apoptosis; caspase-1; gasdermin; inflammasome; inflammatory cell death; innate immune cell death; interferon; necroptosis; pattern recognition receptor; pyroptosis.

Figure 1.. Evolutionary dynamics of NLR genes in the tree of life

A) NLR networks and their complexity/development over evolutionary time from multifunctional ancestors to specialized NLR singletons with dual roles as sensors and helpers, followed by receptor specialization to divide their functions, with distinct NLR proteins taking on sensor and helper roles, and finally functional diversification. Representation was inspired by previous descriptions of NLR networks. B) Phylogenetic distribution of NLR genes per genome among selected organisms representing major phyla across three primary domains: bacteria, archaea, and eukarya (including algae, fungi, plants, and animals). The distribution is mapped on a simplified tree, and branch lengths are not drawn to scale. The scientific names of the organisms used in the tree are indicated here: (i) Bacteria: Steptomyces coelicolor (Steptomyces; Gram positive), Rickettsia conorii (Rickettsia; Gram negative), (ii) Archaea: Methanothrix soehngenii (methanogenic archaea), Prometheoarchaeum syntrophicum (asgard), (iii) Algae: Chromochloris zofingiensis (green algae), (iv) Fungi: Cenococcum geophilum (sac fungi; Ascomycota), Agaricus bisporus (mushroom; Basidiomycota), (v) Plants: Land plants: Physcomitrella patens (earthmoss; Bryophyta), Marchantia polymorpha (liverwort; Marchantiophyta), Vascular plants: Selaginella moellendorffii (spikemoss; Lycophyte), Ceratopteris richardii (fern; Monilophyte), Flowering plants: Malus domestica (apple; Eudicot angiosperm), Arabidopsis thaliana (Arabidopsis; Eudicot angiosperm), Solanum tuberosum (potato; Eudicot angiosperm), S. lycopersicum (tomato; Eudicot angiosperm), Hordeum vulgare (barley; Monocot angiosperm), Triticum aestivum (wheat; Monocot angiosperm), Oryza sativa (rice; Monocot angiosperm), Zea mays (maize; Monocot angiosperm), Non-flowering plants: Ginkgo biloba (ginko; Gymnosperm), (vi) Animals: Amphimedon queenslandica (sponge; Porifera), Acropora digitifera (coral; Cnidaria), Caenorhabditis elegans (worm; Nematoda), Hydra magnipapillata (fresh-water polyp; Mollusca), Drosophila melanogaster (fruit fly; Arthropoda), Capitella teleta (bristle worm; Annelida), Strongylocentrotus purpuratus (sea urchin; Echinodermata), Ciona intestinalis (sea squirt; Tunicata), Branchiostoma floridae (lancelet; Leptocardii), Mus musculus (mouse; Rodentia), Homo sapiens (human; Primates), Takifugu rubripes (Japanese puffer; Tetraodontiformes), Cyprinus carpio (carp; Cypriniformes) and Danio rerio (zebrafish; Cypriniformes). The number of NLR genes were extracted from multiple reports. Representation was inspired by previous tree representations; tree designs were adapted from SVG SILH source (https://svgsilh.com) and modified using Biorender.

Figure 2.. NLR architecture

Domains of nucleotide-binding and oligomerization (NOD)-like receptors (NLRs), or nucleotide-binding domain (NBD) and leucine-rich repeat (LRR) proteins, are shown for human and mouse isoforms. Five different subgroups are classified in human and mouse NLR families based on N-terminal domains. These include NLRA (NLRs containing an acidic transactivation domain, AD); NLRB (NLRs containing a baculovirus inhibitor of apoptosis repeat, BIR), also known as NAIPs; NLRC (NLRs containing a caspase activation and recruitment domain, CARD); NLRP (NLRs containing a pyrin domain, PYD); and NLRX (NLRs containing a domain with no similarity to known NLR subfamily members; currently assigned as ‘X’ in the nomenclature). NLRC1 and NLRC2 are more commonly known as NOD1 and NOD2, respectively, and this terminology is reflected here. NLRP3 and NLRP12 are unique in having the full fish-specific NACHT-associated (FISNA) domain, while NLRP6 has a similar domain with only some of the FISNA characteristics. Domain boundaries were extracted from NCBI GenPept entries and are shown from human sequence, unless otherwise indicated for mouse. The domains are not shown to scale. Abbreviations: CIITA, MHC class II transactivator; FIIND, domain with function to find, also called the autoproteolytic domain; NAIP, neuronal apoptosis inhibitor protein; PST, proline/serine/threonine. a Form-III and IV of CIITA lack the N-terminal CARD domain, and form-II shows low transcriptional activity. b Naip3 exists as a pseudogene. c Nlrp4d exists as a pseudogene.

Figure 3.. NLRs in inflammasome and PANoptosomes

Nucleotide-binding and oligomerization (NOD)-like receptors (NLRs) can act as key sensors in multi-protein cell death complexes, including inflammasomes and PANoptosomes, in response to diverse pathogenic and sterile triggers. A) The result of inflammasome complex formation is caspase-1 (CASP1) autoproteolysis and activation, leading to its cleavage of gasdermin D (GSDMD) to induce membrane pore formation and pro–IL-1β and pro–IL-18 to release their mature forms (IL-1β and IL-18). Non-NLR proteins, including AIM2 and Pyrin, can also induce canonical inflammasome formation. B) The result of PANoptosome complex formation is the activation of multiple caspases and receptor-interacting protein kinases (RIPKs) to drive inflammatory cell death, PANoptosis. Abbreviations: ASC, apoptosis-associated speck-like protein containing a caspase activation and recruitment domain; CASP6, caspase-6; CASP8, caspase-8; DAMPs, damage-associated molecular patterns; DPP8/9, dipeptidyl peptidases 8 and 9; HSV1, herpes simplex virus 1; IAV, influenza A virus; IFN, interferon; LPS, lipopolysaccharide; NAIPs, NLR family of apoptosis inhibitory proteins; NEI, nuclear export inhibitor; PAMPs, pathogen-associated molecular patterns; TAK1i, transforming growth factor-β-activated kinase 1 inhibitor; ZBP1, Z-DNA binding protein 1. Figure prepared using Biorender.