Comparative Genomic and Sequence Analysis Provides Insight into the Molecular Functionality of NOD1 and NOD2

Department of Biochemistry, University of Cambridge , Cambridge , UK.
Frontiers in Immunology 10/2013; 4:317. DOI: 10.3389/fimmu.2013.00317
Source: PubMed


Amino acids with functional or key structural roles display higher degrees of conservation through evolution. The comparative analysis of protein sequences from multiple species and/or between homologous proteins can be highly informative in the identification of key structural and functional residues. Residues which in turn provide insight into the molecular mechanisms of protein function. We have explored the genomic and amino acid conservation of the prototypic innate immune genes NOD1 and NOD2. NOD1 orthologs were found in all vertebrate species analyzed, whilst NOD2 was absent from the genomes of avian, reptilian and amphibian species. Evolutionary trace analysis was used to identify highly conserved regions of NOD1 and NOD2 across multiple species. Consistent with the known functions of NOD1 and NOD2 highly conserved patches were identified that matched the Walker A and B motifs and provided interaction surfaces for the adaptor protein RIP2. Other patches of high conservation reflect key structural functions as predicted by homology models. In addition, the pattern of residue conservation within the leucine-rich repeat (LRR) region of NOD1 and NOD2 is indicative of a conserved mechanism of ligand recognition involving the concave surface of the LRRs.

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Available from: Tom P Monie, Mar 18, 2014
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    • "An additional aspect of this interface is that it includes two residues of NOD1 (Asn36 and Glu56) that are highly conserved across evolution, supporting the idea that it may be used for important protein interactions such as that of Ub described here [36]. Moreover, mutation of Gln56 compromises the ability of NOD1 to activate its downstream effector kinase RIP2 [37], through a yet unknown mechanism. "
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    ABSTRACT: The Caspase Recruitment Domain (CARD) from the innate immune receptor NOD1 was crystallized with Ubiquitin (Ub). NOD1 CARD was present as a helix-swapped homodimer similar to other structures of NOD1 CARD, and Ub monomers formed a homodimer similar in conformation to Lys48-linked di-Ub. The interaction between NOD1 CARD and Ub in the crystal was mediated by novel binding sites on each molecule. Comparisons of these sites to previously identified interaction surfaces on both molecules were made along with discussion of their potential functional significance.
    PLoS ONE 08/2014; 9(8):e104017. DOI:10.1371/journal.pone.0104017 · 3.23 Impact Factor
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    • "Previous studies and ongoing work in our own laboratory have investigated the functional role of residues in the NOD1 CARD [15,16], but none have explicitly addressed phosphorylation. Given the importance of CARD phosphorylation in the regulation of RIG-I and MDA-5 signalling we hypothesised that serine 7 in human NOD1 could be a possible candidate for the regulation of NOD1 signalling and that the NOD1 SNP S7N may consequently disrupt receptor function. "
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    ABSTRACT: Activation and signal transduction in the Nucleotide binding, leucine-rich repeat containing receptor (NLR) family needs to be tightly regulated in order to control the inflammatory response to exogenous and endogenous danger signals. Phosphorylation is a common cellular mechanism of regulation that has recently been shown to be important in signalling in another family of cytoplasmic pattern recognition receptors, the RIG-I like receptors. In addition, single nucleotide polymorphisms can alter receptor activity, potentially leading to dysfunction and/or a predisposition to inflammatory barrier diseases. We have computationally analysed the N-terminus of NOD1 and found seven theoretical phosphorylation sites in, or immediately before, the NOD1 Caspase Activation Domain (CARD). Two of these, serine 7 and tyrosine 49 are also found as rare polymorphisms in the African-American population and European-American populations respectively. Mutating serine 7 to either an aspartic acid or an asparagine to mimic the potential impact of phosphorylation or the polymorphism respectively did not affect the response of NOD1 to ligand-mediated NFkappaB signalling. The NOD1 polymorphism S7N does not interfere with receptor function in response to ligand stimulation.
    BMC Research Notes 03/2014; 7(1):124. DOI:10.1186/1756-0500-7-124
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    ABSTRACT: The innate immune system is composed of a diverse set of host defense molecules, physical barriers, and specialized leukocytes and is the primary form of immune defense against environmental insults. Another crucial role of innate immunity is to shape the long-lived adaptive immune response mediated by T and B lymphocytes. The activation of pattern recognition receptors (PRRs) from the Toll-like receptor family is now a classic example of innate immune molecules influencing adaptive immunity, resulting in effective antigen presentation to naïve T cells. More recent work suggests that the activation of another family of PRRs, the NOD-like receptors (NLRs), induces a different set of innate immune responses and accordingly, drives different aspects of adaptive immunity. Yet how this unusually diverse family of molecules (some without canonical PRR function) regulates immunity remains incompletely understood. In this review, we discuss the evidence for and against NLR activity orchestrating adaptive immune responses during infectious as well as non-infectious challenges.
    Frontiers in Immunology 12/2013; 4:486. DOI:10.3389/fimmu.2013.00486
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