Subfamilies of NLRs can be distinguished on the basis of the other protein domains they contain. The NOD subfamily has an amino-terminal caspase recruitment domain (CARD) (Fig. 3.17). CARD was initially recognized in a family of proteases called caspases (for cysteine-aspartic acid proteases), which are important in many intracellular pathways, including those leading to cell death by apoptosis. CARD is structurally related to the TIR death domain in MyD88 and can dimerize with CARD domains on other proteins to induce signaling (Fig. 3.18). NOD proteins recognize fragments of bacterial cell-wall peptidoglycans, although it is not known whether this occurs through direct binding or via accessory proteins. NOD1 senses γ-glutamyl diaminopimelic acid (iE-DAP), a breakdown product of peptidoglycans of Gram-negative bacteria such as Salmonella and some Gram-positive bacteria such as Listeria,
Pattern recognition by cells of the innate immune system.
LRR domain cytoplasm RIP2 RIP2 NF˜B I˜B Binding of bacterial ligands to NOD proteins induces recruitment of RIP2, which activates TAK1, leading to NF˜B activation NOD proteins reside in the cytoplasm in an inactive form CARD XIAP cIAP1/2 NOD CARD NOD intracellular bacteria, muramyl dipeptide or iE-DAP TAB1/2 NEMO polyubiquitin TAK1 IKK°IKK˛
Fig. 3.17 Intracellular NOD proteins sense the presence of bacteria by recognizing bacterial peptidoglycans and activate NFκB to induce the expression of pro-inflammatory genes.
whereas NOD2 recognizes muramyl dipeptide (MDP), which is present in the peptidoglycans of most bacteria. NOD ligands may enter the cytoplasm as a result of intracellular infection, but may also be transported from materials captured by endocytosis, since mice lacking an oligopeptide transporter (SLC15A4) that is present in lysosomes have greatly reduced responses to NOD1 ligands.
When NOD1 or NOD2 recognizes its ligand, it recruits the CARD-containing serine–threonine kinase RIP2 (also known as RICK and RIPK2) (see Fig. 3.17). RIP2 associates with the E3 ligases cIAP1, cIAP2, and XIAP, whose activity generates a polyubiquitin scaffold as in TLR signaling. This scaffold recruits TAK1 and IKK and results in activation of NFκB as shown in Fig. 3.15. NFκB then induces the expression of genes for inflammatory cytokines and for enzymes involved in the production of nitric oxide (NO), which is toxic to bacteria and intracellular parasites. In keeping with their role as sensors of bacterial components, NOD proteins are expressed in cells that are routinely exposed to bacteria. These include epithelial cells forming the barrier that bacteria must cross to establish an infection in the body, and the macrophages and dendritic cells that ingest bacteria that have succeeded in entering the body. Macrophages and dendritic cells express TLRs as well as NOD1 and NOD2, and are activated by both pathways. In epithelial cells, NOD1 is an important activator of responses against bacterial infections, and NOD1 may also function as a systemic activator of innate immunity. It seems that peptidoglycans from intestinal microbiota are transported via blood in amounts sufficient to