MR1 is an MHC class Ib molecule that presents small metabolite antigens (Ags) derived from vitamin B metabolism. Conserved ligands derived from microbial riboflavin (Vitamin B2) biosynthesis have been shown to be T cell agonists, activating a unique subset of T cells called mucosal-associated invariant T (MAIT) cells. MAIT cells are highly abundant in humans, accounting for up to 10% of circulating T cells. They are defined by expression of a semi-invariant alpha-beta T cell receptor (TCR) that imbues pattern-recognition-like detection of MR1-presented Ags. Thus MAIT cells are emerging as key players in antimicrobial immunity.

Here, using MR1-Ag tetramers, we enumerate and phenotypically characterise human blood MAIT cells. We also identify and characterise atypical populations of MR1-restricted T cells, spanning both the alpha-beta and gamma-delta T cell lineages that exhibit distinct phenotypic features and Ag-reactivities to that of conventional MAIT cells. Finally, we provide a molecular basis for MR1-Ag recognition by these diverse MR1-restricted T cell subsets.