Mucosa-associated invariant T (MAIT) cells recognise vitamin B metabolites presented by the molecule MR1.
Artwork by: Erica Tandori

“We generated multiple altered metabolite ligands and determined their structures in the context of mr1 and the tcr to develop a generalised framework for mait cell antigen recognition. These discoveries could pave the way for development of novel t cell therapy.”

In 2012 and 2014, Imaging CoE Centre scientists made the startling discovery that an abundant T cell population, termed mucosal-associated invariant T (MAIT) cells, was activated by metabolites of vitamin B2 (called riboflavin) (Nature 2012 & 2014).



Armed with this information, the field is now empowered to identify and understand the roles of MAIT cells in mammalian homeostasis, health and disease. To further enable this, Imaging CoE scientists have developed novel biochemical reagents: MR1 tetramer proteins, MR1-binding fluorescent ligands and MAIT cell-binding fluorescent ligands. These have enabled the identification, tracking and phenotypic characterisation of antigens; their initial target MR1 on antigen presenting cells; and their eventual target MAIT cells that have important immunoregulatory properties in mammals.

Work in this area has helped establish:

  1. The discovery of a patient homozygous for a rare Arg31His. (The patient has a mutation in MR1 and history of difficult-to-treat viral and bacterial infections.) Here, MR1R9H was unable to present the potent microbially derived MAIT cell stimulatory ligand whereby the stimulatory ligand could not bind due to the mutation lying within. This caused structural perturbation to the ligand-binding domain of MR1. While MR1R9H could bind and be upregulated by a MAIT cell inhibitory ligand, the patient lacked circulating MAIT cells. This study showed the importance of the stimulatory ligand for MAIT cell selection in humans (Howson et al. Science Immunology 2020).
  2. We designed 20 synthetic analogues of the potent MAIT agonist 5-OP-RU, termed ‘altered metabolite ligands’ (AMLs), to dissect the impact of different antigen components on the human MAIT-MR1 axis. Through the generation and detailed analysis of 11 crystal structures of TCR and TCR-MR1-Ags complexes, as well as chemistry and functional immunological aspects, a focused network of nano-connections termed ‘MAIT Interaction Triad’ was discovered to fine-tune MAIT immune response. This study defined the basis for which the MAIT TCR can differentially recognise AMLs, thereby providing insight into MAIT cell antigen specificity and potency (Awad et al., Nature Immunology 2020).
  3. While previously described MR1 ligands facilitate translocation of endoplasmic reticulum-resident MR1 to the cell surface, we describe the first non-microbial ligand, 3-[(2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-yl)formamido] propanoic acid, DB28, and its ester analogue NV18.1, which retain MR1 in the endoplasmic reticulum in an immature ligand-receptive form and competitively inhibit stimulatory ligands. We provide the molecular and functional basis underpinning the interactions of this new class of ligands with MR1 (Salio*, Awad*, Veerapen* et al, PNAS 2020).
  4. We report the crystal structures of the unliganded TRAV12-2+ TCR (termed D462-E4) TCR and its complex with MR1 presenting the riboflavin-based antigen, 5-OP-RU. The D462-E4 T cell clone detected the infection of both riboflavin-producing microbes and riboflavin-auxotroph Streptococcus pyogenes in a MR1 dependent manner. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F’-pocket of MR1, whereby the CDR3β loop surrounded and projected into the F’-pocket. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities (Awad et al., Journal of Biological Chemistry 2020).
  5. In related study of metabolite recognition, it has been known for several years that microbial and tumour-derived phosphoantigen metabolites are targets of Vδ2 Vγ9+ γδ T cells, but the molecular basis for this recognition and the target molecules involved was unknown. In a project led by CI Professor Dale Godfrey’s team, including co-senior investigator, AI Dr. Adam Uldrich, we determined that phosphoantigen recognition requires a direct interaction between the Vδ2Vγ9 TCR and a cell surface protein, butyrophilin 2A1. This molecule is expressed by target cells and this paves the way for understanding the role that these γδ T cells play in immunity to microbial and tumour-derived phosphoantigens (Rigau et al. Science 2020).


  1. Investigated MAIT cell antigen recognition and activation.
  2. Investigated MR1-restricted T cell antigen recognition, activation and homeostasis.
  3. Determined crystal structures for antigen-MR1 binary complexes.
  4. Developed a binding assay for optimising antigen-MR1 affinities.
  5. Designed and developed inhibitors of MAIT cell activation.
  6. Probed the mechanisms of antigen presentation and MR1 trafficking.
  7. Assessed the immunological impacts of MAIT activation in vitro and in vivo.
  8. Determined the molecular target underlying phosphoantigen recognition by γδ T cells.