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Intracellular pathogens lose many metabolic genes during their evolution from free-living bacteria, but the pathogenic consequences of their altered metabolic programs on host immunity are poorly understood. Here, we show that a pathogenic strain of

Intracellular pathogens lose many metabolic genes during their evolution from free-living bacteria, but the pathogenic consequences of their altered metabolic programs on host immunity are poorly understood. Here, we show that a pathogenic strain of Francisella tularensis subsp. tularensis (FT) has five amino acid substitutions in RibD, a converting enzyme of the riboflavin synthetic pathway responsible for generating metabolites recognized by mucosal-associated invariant T (MAIT) cells. Metabolites from a free-living strain, F. tularensis subsp. novicida (FN), activated MAIT cells in a T-cell receptor (TCR)–dependent manner, whereas introduction of FT-type ribD to the free-living strain was sufficient to attenuate this activation in both human and mouse MAIT cells. Intranasal infection in mice showed that the ribDFT-expressing FN strain induced impaired Th1-type MAIT cell expansion and resulted in reduced bacterial clearance and worsened survival compared with the wild-type free-living strain FN. These results demonstrate that F. tularensis can acquire immune evasion capacity by alteration of metabolic programs during evolution.

The immune system must discriminate between beneficial and harmful microbes in the gut, and failure to maintain a proper balance of immune responsiveness and immune tolerance to gut microbes can lead to intestinal pathology. In particular, inflammatory bowel diseases such as Crohn's Disease and ulcerative colitis are thought to be the result of aberrant immune responses targeting commensal bacteria normally present in the gut lumen. The early events that break steady-state tolerance and trigger an immune response directed to commensal bacterial antigens remain poorly understood. Using a peptide:MHC-II tetramer-based enrichment approach, we characterized endogenous CD4+ T cells specific for Cbir1, a flagellin antigen from commensal bacteria present in the gut of normal mice. Our data show that endogenous Cbir1-specific T cells develop in the thymus of normal mice at the double positive stage. These cells survive negative selection and populate the peripheral lymphoid organs without becoming activated. Following immunization with their cognate antigen, they undergo massive proliferation and upregulate activation markers. Despite the presence of Cbir1 in the gut lumen, Cbir1-specific T cells in the lamina propria do not differentiate into regulatory T cells, nor do they induce colitis in normal mice. These data suggest that immune ignorance, rather than regulatory T cell induction, is a major mechanism of immune tolerance to commensal bacteria flagellin in the gut.

The impact of major histocompatibility complex (MHC) phenotype on the shaping of the peripheral naive T cell repertoire in humans remains unknown. Here we exploited a pMHC multimer-based sorting approach to analyze the impact of expression of a given human leukocyte Ag (HLA) class I allele on the frequency and quality of peripheral blood and thymic T cells directed against immunodominant self, viral and tumor antigens presented by a human MHC class I allele (HLA-A*02, referred to as A2) in individuals expressing or not this allele. Naive T cell frequencies varied from one antigen specificity to another but were restrained for a given specificity. While A2-restricted T cells showed similar repertoire features and antigenic avidities in A2+ and A2- donors, A2 expression had either a positive, neutral or negative impact on the frequency of A2-restricted naive CD8 T cells, depending on their fine specificity. We also identified in all donors CD4 T cells specific for A2/peptide complexes, whose frequencies were not affected by MHC class I expression, but nevertheless correlated with those of their naive CD8 T cell counterparts. Therefore both selection by self MHC and inherent TCR reactivity regulate the frequency of human naive T cell precursors. Moreover this study also suggests that T cell repertoire shaping by a given self MHC allele is dispensable for generation of immunodominant T cell responses restricted by this particular allele.

Innate-like T cells display characteristics of both innate lymphoid cells (ILCs) and mainstream αβ T cells, leading to overlapping functions of innate-like T cells with both subsets. In this review, we show that although innate-like T cells are probably present in all vertebrates, their main characteristics are much better known in amphibians and mammals. Innate-like T cells encompass both γδ and αβ T cells. In mammals, γδ TCRs likely coevolved with molecules of the butyrophilin family they interact with, whereas the semi-invariant TCRs of iNKT and mucosal-associated invariant T cells are evolutionarily locked with their restricting MH1b molecules, CD1d and MR1, respectively. The strong conservation of the Ag recognition systems of innate-like T cell subsets despite similar effector potentialities supports that each one fulfills nonredundant roles related to their Ag specificity.