The nucleotide-binding oligomerization domain receptors, in short NOD-like receptors (NLRs) are intracellular sensors of PAMPs that enter the cell via phagocytosis or pores and DAMPs that are associated with cell stress. They are part of pattern recognition receptors and play key roles in regulation of innate immune response. NLRs can cooperate with Toll-like receptors and regulate inflammatory and apoptotic response. They are found in lymphocytes, macrophages, dendritic cells and also in nonimmune cells, for example in epithelium. NLRs are highly conserved through evolution. Their homologs have been discovered in many different animal species (APAF1)  and also in the plant kingdom (disease-resistance R protein).
NLRs contain 3 domains – central NACHT (NOD or NBD – nucleotide-binding domain) domain, which is common to all NLRs, most of NLRs have also C-terminal leucine-rich repeat (LRR) and variable N-terminal interaction domain. NACHT domain mediates ATP-dependent self-oligomerization and LRR senses the presence of ligand. N-terminal domain is responsible for homotypic protein-protein interaction and it can consist of caspase recruitment domain (CARD), pyrin domain (PYD), acidic transactivating domain or baculovirus inhibitor repeats (BIRs).
Nomenclature and system
Names as CATERPILLER, NOD, NALP, PAN, NACHT, PYRAF were used to describe the NLRs family. The nomenclature was unified by the HUGO Gene Nomenclature Committee in 2008. The family was characterized as NLRs to provide description of the families features – NLR means nucleotide-binding domain and leucine-rich repeat containing gene family.
This system divides NLRs into 4 subfamilies based on the type of N-terminal domain:
- NLRA (A for acidic transactivating domain): CIITA
- NLRB (B for BIRs): NAIP
- NLRC (C for CARD): NOD1, NOD2, NLRC3, NLRC4, NLRC5
- NLRP (P for PYD): NLRP1, NLRP2, NLRP3, NLRP4, NLRP5, NLRP6, NLRP7, NLRP8, NLRP9, NLRP10, NLRP11, NLRP12, NLRP13, NLRP14 
On the other hand, NLRs can be divided into 3 subfamilies with regard to their phylogenetic relationships:
- NODs: NOD1, NOD2, NOD3 (NLRC3), NOD4 (NLRC5), NOD5 (NLRX1), CIITA
- NLRPs (also called NALPs): NLRP1, NLRP2, NLRP3, NLRP4, NLRP5, NLRP6, NLRP7, NLRP8, NLRP9, NLRP10, NLRP11, NLRP12, NLRP13, NLRP14
- IPAF: IPAF (NLRC4), NAIP 
The well-described receptors are NOD1 and NOD2. The recognition of their ligands recruits oligomerization of NACHT domain and CARD-CARD interaction with CARD-containing serine-threonin kinase RIP2 which leads to activation of RIP2. RIP2 mediates the recruitment of kinase TAK1 which phosphorylates and activates IκB kinase. The activation of IκB kinase results in the phosphorylation of inhibitor IκB which releases NF-κB and its nuclear translocation. NF-κB then activates expression of inflammatory cytokines. Mutations in NOD2 are associated with the Crohn’s disease  or Blau syndrome.
NOD1 and NOD2 recognize peptidoglycan motifs from bacterial cell which consists of N-acetylglucosamine and N-acetylmuramic acid. These sugar chains are cross-linked by peptide chains that can be sensed by NODs. NOD1 recognizes a molecule called meso-diaminopimelic acid (meso-DAP) mostly found in Gram-negative bacteria (for example Helicobacter pylori, Pseudomonas aeruginosa). NOD2 proteins can sense intracellular muramyl dipeptide (MDP), typical for bacteria such as Streptococcus pneumoniae or Mycobacterium tuberculosis.
Subfamilies NALPs and IPAF
NALPs and IPAF subfamilies are involved in the formation of the inflammasome. The best characterized inflammasome is NLRP3, the activation through PAMPs or DAMPs leads to the oligomerization. The pyrin domain of NLRs binds to an adaptor protein ASC (PYCARD) via PYD-PYD interaction. ASC contains PYD and CARD domain and links the NLRs to inactive form of caspase 1 through the CARD domain. All these protein-protein interaction form a complex called the inflammasome. The aggregation of the pro-caspase-1 causes the autocleavage and formation of an active enzyme. Caspase-1 is important for the proteolytic processing of the pro-inflammatory cytokines IL-1β and IL-18. NLRP3 mutations are responsible for the autoinflammatory disease familial cold autoinflammatory syndrome or Muckle-Wells syndrome.
There are three well-characterized inflammasomes – NLRP1, NLRP3 and IPAF. The formation of NLRP3 inflammasome can be activated by PAMPs such as microbial toxins (for example alpha-toxin Staphylococcus aureus) or whole pathogens, for instance Candida albicans, Saccharomyces cerevisiae, Sendai virus, Influenza. NLRP3 recognize also DAMPs which indicate stress in the cell. The danger molecule can be extracellular ATP, extracellular glucose, crystals of monosodium urate (MSU), calcium pyrophosphate dihydrate (CPPD), alum, cholesterol or environmental irritants – silica, asbestos, UV irradiation and skin irritants. The presence of these molecules causes a production of ROS and K+ efflux. NLRP1 recognizes lethal toxin from Bacillus anthracis and muramyl dipeptide. IPAF senses flagellin from Salmonella typhimurium, Pseudomonas aeruginosa, Listeria monocytogenes.
Notes and references
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