Hyperconservation of theN-Formyl Peptide Binding Site ofM3: Evidence thatM3Is an Old Eutherian Molecule with Conserved Recognition of a Pathogen-Associated Molecular Pattern

Abstract

The mouse MHC class I-b molecule H2-M3 has unique specificity for N-formyl peptides, derived from bacteria (and mitochondria), and is thus a pathogen-associated molecular pattern recognition receptor (PRR). To test whether M3 was selected for this PRR function, we studied M3 sequences from diverse murid species of murine genera Mus, Rattus, Apodemus, Diplothrix, Hybomys, Mastomys, and Tokudaia and of sigmodontine genera Sigmodon and Peromyscus. We found that M3 is highly conserved, and the 10 residues coordinating the N-formyl group are almost invariant. The ratio of nonsynonymous and synonymous substitution rates suggests the Ag recognition site of M3, unlike the Ag recognition site of class I-a molecules, is under strong negative (purifying) selection and has been for at least 50–65 million years. Consistent with this, M3 α1α2 domains from Rattus norvegicus and Sigmodon hispidus and from the “null” allele H2-M3b specifically bound N-formyl peptides. The pattern of nucleotide substitution in M3 suggests M3 arose rapidly from murid I-a precursors by an evolutionary leap (“saltation”), perhaps involving intense selective pressure from bacterial pathogens. Alternatively, M3 arose more slowly but prior to the radiation of eutherian (placental) mammals. Older dates for the emergence of M3, and the accepted antiquity of CD1, suggest that primordial class I MHC molecules could have evolved originally as monomorphic PRR, presenting pathogen-associated molecular patterns. Such MHC PRR molecules could have been preadaptations for the evolution of acquired immunity during the early vertebrate radiation.

Polymorphisms in CD1d affect antigen presentation and the activation of CD1d-restricted T cells

“…DNA sequence analysis revealed that the allelic differences of CD1D genes are much lower than those in MHC class Ia genes, suggesting strong conservation within CD1D genes. The divergence among CD1d alleles is comparable with that seen in MHC class Ib molecules that perform specialized immune functions, including TL, M3, and Qa-1 (29)(30)(31).…”

Innate microbial sensors and their relevance to allergy

“…The MHC class I-b molecule of mice is a specific binding receptor for microbial n-formyl peptides, thereby forming an intriguing link between MHC class I and microbial PRR-type recognition. 82 Other known cytoplasmic PRRs include retinoic acid-inducible gene-1 and melanoma differentiation-associated gene-5, helicases that recognize viral double-stranded RNA and mediate antiviral immune responses to different double-stranded RNA viruses. 83 …”

MR1 antigen presentation to mucosal-associated invariant T cells was highly conserved in evolution

“…S3). Purifying selection also has been implicated among murid species in the evolution of H2-M3 orthologs that bind peptide ligands containing a conserved N-formylated methionine as presented to CD8 ϩ T cells, as well as among primate HLA-E orthologs that present conserved class Ia signal peptides to NK cells (5,14,15). Thus, there are clear precedents implicating purifying selection resulting in the presentation of molecular patterns.…”