Table 1.
Research articles with data directly addressing NOD2 and mycobacteriaa.
Fig 1.
These structural representations were generated from UniProt entry Q9HC29 (“NOD2_HUMAN”) folded with AlphaFold. Approximately 180° of rotation separates the images from the top and bottom rows. (A) Ribbon structure of NOD2 with AlphaFold per-residue confidence score (pLDDT) in range from 0 to 100 (low to high confidence). (B) Ribbon and (C) space-filling models of AlphaFold NOD2 illustrated using UCSF ChimeraX based on UniProt domain annotation. NOD2 has 4 domains: 2 CARDs, 1 NACHT/NBD, and 1 LRR domain. In Crohn’s disease, some patients have a frameshift variant where the protein is foreshortened by 34 amino acids. This missing region is shown in mauve. CARD, caspase recruitment domain; LRR, leucine-rich repeat; NBD, nucleotide-binding domain; NOD2, Nucleotide-binding Oligomerization Domain-containing 2.
Fig 2.
The cell envelope of mycobacteria and mycobacterial peptidoglycan.
(A) Cross-sectional cartoon of the mycobacterial envelope, showing major regions in approximate relative size to each other. (B) Parallel strands of mycobacterial PGN containing MurNGc, MurNAc, and GlcNAc, with peptides partially cross-linked (red lines). (C) N-acetyl MDP, the minimal PGN fragment recognized by NOD2, common to most bacteria. The sugar and amino acids are separated by differently colored backgrounds. (D) N-glycolyl MDP, the distinct NOD2 ligand of mycobacteria, with the additional hydroxy group from N-glycolylation highlighted in red. The sugar and amino acids are separated by differently colored backgrounds. GlcNAc, N-acetyl glucosamine; MDP, muramyl dipeptide; MurNAc, N-acetyl muramic acid; MurNGc, N-glycolyl muramic acid; NOD2, Nucleotide-binding Oligomerization Domain-containing 2; PGN, peptidoglycan.
Fig 3.
NOD2 signaling during mycobacterial infection.
Cartoon depicting mycobacteria (fuchsia bacilli) being engulfed and sensed by a macrophage through NOD2. Muropeptides including the MDP motif exit the phagosome via a SLC15A family transporter. Upon entering the cytosol, MDP is phosphorylated by NAGK and subsequently sensed via NOD2, which has been recruited to the membrane by palmitoylation from ZDHHC5 (not shown). RIPK2 is phosphorylated and ubiquitinated, mediating signaling cascades and culminating in NF-κB and MAPK transcription factors translocating to the nucleus to regulate inflammatory gene transcription. Various immune mediators, both intracellular and extracellular in activity, result from NOD2 signaling. The degree of evidence for involvement of the depicted elements in the NOD2-dependent immune response to mycobacteria is indicated semiquantitatively (no data, limited/unclear, and many sources). ATG16L1, autophagy-related 16 like 1; IAP, inhibitor of apoptosis; iNOS, inducible nitric oxide synthase; IRF, interferon regulatory factor; IRGM, immunity-related GTPase M; KC, KC(CXCL1); LRRK2, leucine-rich repeat kinase 2; LUBAC, linear ubiquitin chain assembly complex; MAPK, mitogen-activated protein kinase; MDP, muramyl dipeptide; NAGK, N-acetylglucosamine kinase; NOD2, Nucleotide-binding Oligomerization Domain-containing 2; RIPK2, receptor-interacting protein kinase 2; TBK1, TANK-binding kinase 1; TNF, tumor necrosis factor; TRAF, tumor necrosis factor receptor-associated factor.