Abstract
The T cell repertoire is generated during thymic development in preparation for the response to antigens from pathogens. The T cell repertoire is shaped by positive selection, which requires recognition by the T cell antigen receptor (TCR) of complexes of self peptide and major histocompatibility complex proteins (self-pMHC) with low affinity, and negative selection, which eliminates T cells with TCRs that recognize self-pMHC with high affinity. This generates a repertoire with low affinity for self-pMHC but high affinity for foreign antigens. The TCR must successfully engage both of these ligands for development, homeostasis and immune responses. This review discusses mechanisms underlying the interaction of the TCR with peptide–major histocompatibility complex ligands of varying affinity and highlights signaling mechanisms that enable the TCR to generate different responses to very distinct ligands.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
References
Smith-Garvin, J.E., Koretzky, G.A. & Jordan, M.S. T cell activation. Annu. Rev. Immunol. 27, 591–619 (2009).
Fraser, I.D. & Germain, R.N. Navigating the network: signaling cross-talk in hematopoietic cells. Nat. Immunol. 10, 327–331 (2009).
Hogquist, K.A. et al. Identification of a naturally occurring ligand for thymic positive selection. Immunity 6, 389–399 (1997).
Hu, Q. et al. Specific recognition of thymic self-peptides induces the positive selection of cytotoxic T lymphocytes. Immunity 7, 221–231 (1997).
Lo, W.L. et al. An endogenous peptide positively selects and augments the activation and survival of peripheral CD4+ T cells. Nat. Immunol. 10, 1155–1161 (2009).
Ebert, P.J., Jiang, S., Xie, J., Li, Q.J. & Davis, M.M. An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a. Nat. Immunol. 10, 1162–1169 (2009). References 3–6 describe endogenous self peptides that mediate positive selection of CD4+ and CD8+ TCR-transgenic T cells.
Evavold, B.D. & Allen, P.M. Separation of IL-4 production from Th cell proliferation by an altered T cell receptor ligand. Science 252, 1308–1310 (1991). This study, examining T cell responses to APLs, discovered the different signaling abilities of TCRs.
Hogquist, K.A. et al. T cell receptor antagonist peptides induce positive selection. Cell 76, 17–27 (1994). This study provided the first evidence of specific recognition of presented peptide antigens in positive selection.
Rudolph, M.G., Stanfield, R.L. & Wilson, I.A. How TCRs bind MHCs, peptides, and coreceptors. Annu. Rev. Immunol. 24, 419–466 (2006).
Zerrahn, J., Held, W. & Raulet, D.H. The MHC reactivity of the T cell repertoire prior to positive and negative selection. Cell 88, 627–636 (1997). This study examined the alloreactive frequency of preselection thymocytes, providing the first evidence for germline affinity of the TCR for MHC.
Feng, D., Bond, C.J., Ely, L.K., Maynard, J. & Garcia, K.C. Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon'. Nat. Immunol. 8, 975–983 (2007).
Dai, S. et al. Crossreactive T cells spotlight the germline rules for αβ T cell-receptor interactions with MHC molecules. Immunity 28, 324–334 (2008).
Scott-Browne, J.P., White, J., Kappler, J.W., Gapin, L. & Marrack, P. Germline-encoded amino acids in the αβ T-cell receptor control thymic selection. Nature 458, 1043–1046 (2009).
Morris, G.P., Ni, P.P. & Allen, P.M. Alloreactivity is limited by the endogenous peptide repertoire. Proc. Natl. Acad. Sci. USA 108, 3695–3700 (2011).
Yin, L. et al. A single T cell receptor bound to major histocompatibility complex class I and class II glycoproteins reveals switchable TCR conformers. Immunity 35, 23–33 (2011).
Wu, L.C., Tuot, D.S., Lyons, D.S., Garcia, K.C. & Davis, M.M. Two-step binding mechanism for T-cell receptor recognition of peptide MHC. Nature 418, 552–556 (2002).
Felix, N.J. et al. Alloreactive T cells respond specifically to multiple distinct peptide-MHC complexes. Nat. Immunol. 8, 388–397 (2007). This study described the phenomenon of polyspecificity, demonstrating that a single TCR can specifically recognize multiple peptide antigens presented by a given MHC.
Garcia, K.C., Adams, J.J., Feng, D. & Ely, L.K. The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat. Immunol. 10, 143–147 (2009).
Huseby, E.S. et al. How the T cell repertoire becomes peptide and MHC specific. Cell 122, 247–260 (2005).
Matsui, K. et al. Low affinity interaction of peptide-MHC complexes with T cell receptors. Science 254, 1788–1791 (1991).
Huang, J. et al. The kinetics of two-dimensional TCR and pMHC interactions determine T-cell responsiveness. Nature 464, 932–936 (2010).
Huppa, J.B. et al. TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity. Nature 463, 963–967 (2010).
Sloan-Lancaster, J., Evavold, B.D. & Allen, P.M. Induction of T-cell anergy by altered T-cell-receptor ligand on live antigen-presenting cells. Nature 363, 156–159 (1993).
Sloan-Lancaster, J., Shaw, A.S., Rothbard, J.B. & Allen, P.M. Partial T cell signaling: altered phospho-ζ and lack of zap70 recruitment in APL-induced T cell anergy. Cell 79, 913–922 (1994).
Hogquist, K.A., Jameson, S.C. & Bevan, M.J. Strong agonist ligands for the T cell receptor do not mediate positive selection of functional CD8+ T cells. Immunity 3, 79–86 (1995).
Sebzda, E. et al. Mature T cell reactivity altered by peptide agonist that induces positive selection. J. Exp. Med. 183, 1093–1104 (1996).
Kersh, E.N., Shaw, A.S. & Allen, P.M. Fidelity of T cell activation through multistep T cell receptor ζ phosphorylation. Science 281, 572–575 (1998).
Kersh, E.N., Kersh, G.J. & Allen, P.M. Partially phosphorylated T cell receptor ζ molecules can inhibit T cell activation. J. Exp. Med. 190, 1627–1636 (1999).
Cahalan, M.D. & Chandy, K.G. The functional network of ion channels in T lymphocytes. Immunol. Rev. 231, 59–87 (2009).
Aivazian, D. & Stern, L.J. Phosphorylation of T cell receptor ζ is regulated by a lipid dependent folding transition. Nat. Struct. Biol. 7, 1023–1026 (2000).
Xu, C. et al. Regulation of T cell receptor activation by dynamic membrane binding of the CD3ɛ cytoplasmic tyrosine-based motif. Cell 135, 702–713 (2008).
Sun, Z.J., Kim, K.S., Wagner, G. & Reinherz, E.L. Mechanisms contributing to T cell receptor signaling and assembly revealed by the solution structure of an ectodomain fragment of the CD3ɛγ heterodimer. Cell 105, 913–923 (2001).
Minguet, S., Swamy, M., Alarcon, B., Luescher, I.F. & Schamel, W.W. Full activation of the T cell receptor requires both clustering and conformational changes at CD3. Immunity 26, 43–54 (2007).
Martínez-Martin, N. et al. Cooperativity between T cell receptor complexes revealed by conformational mutants of CD3ɛ. Sci. Signal. 2, ra43 (2009).
Monks, C.R., Freiberg, B.A., Kupfer, H., Sciaky, N. & Kupfer, A. Three-dimensional segregation of supramolecular activation clusters in T cells. Nature 395, 82–86 (1998).
Grakoui, A. et al. The immunological synapse: a molecular machine controlling T cell activation. Science 285, 221–227 (1999).
Dustin, M.L. & Depoil, D. New insights into the T cell synapse from single molecule techniques. Nat. Rev. Immunol. 11, 672–684 (2011).
Bunnell, S.C. et al. T cell receptor ligation induces the formation of dynamically regulated signaling assemblies. J. Cell Biol. 158, 1263–1275 (2002).
Manz, B.N., Jackson, B.L., Petit, R.S., Dustin, M.L. & Groves, J. T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters. Proc. Natl. Acad. Sci. USA 108, 9089–9094 (2011).
Wülfing, C. et al. Costimulation and endogenous MHC ligands contribute to T cell recognition. Nat. Immunol. 3, 42–47 (2002).
Krogsgaard, M. et al. Agonist/endogenous peptide-MHC heterodimers drive T cell activation and sensitivity. Nature 434, 238–243 (2005). References 40 and 41 describe the participation of self-pMHC complexes in T cell response to agonist pMHC ligands.
Kuhns, M.S. et al. Evidence for a functional sidedness to the αβTCR. Proc. Natl. Acad. Sci. USA 107, 5094–5099 (2010).
Vidal, K., Daniel, C., Hill, M., Littman, D.R. & Allen, P.M. Differential requirements for CD4 in TCR-ligand interactions. J. Immunol. 163, 4811–4818 (1999).
Yachi, P.P., Ampudia, J., Zal, T. & Gascoigne, N.R. Altered peptide ligands induce delayed CD8-T cell receptor interaction–a role for CD8 in distinguishing antigen quality. Immunity 25, 203–211 (2006).
Campi, G., Varma, R. & Dustin, M.L. Actin and agonist MHC-peptide complex-dependent T cell receptor microclusters as scaffolds for signaling. J. Exp. Med. 202, 1031–1036 (2005).
Yokosuka, T. et al. Newly generated T cell receptor microclusters initiate and sustain T cell activation by recruitment of Zap70 and SLP-76. Nat. Immunol. 6, 1253–1262 (2005).
Lillemeier, B.F. et al. TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation. Nat. Immunol. 11, 90–96 (2010).
Purbhoo, M.A. et al. Dynamics of subsynaptic vesicles and surface microclusters at the immunological synapse. Sci. Signal. 3, ra36 (2010).
Monks, C.R., Kupfer, H., Tamir, I., Barlow, A. & Kupfer, A. Selective modulation of protein kinase C-θ during T-cell activation. Nature 385, 83–86 (1997).
Yokosuka, T. et al. Spatiotemporal regulation of T cell costimulation by TCR-CD28 microclusters and protein kinase C θ translocation. Immunity 29, 589–601 (2008).
Choudhuri, K., Wiseman, D., Brown, M.H., Gould, K. & van der Merwe, P.A. T-cell receptor triggering is critically dependent on the dimensions of its peptide-MHC ligand. Nature 436, 578–582 (2005).
Varma, R., Campi, G., Yokosuka, T., Saito, T. & Dustin, M.L. T cell receptor-proximal signals are sustained in peripheral microclusters and terminated in the central supramolecular activation cluster. Immunity 25, 117–127 (2006).
Daniels, M.A. et al. Thymic selection threshold defined by compartmentalization of Ras/MAPK signalling. Nature 444, 724–729 (2006).
Cemerski, S. et al. The stimulatory potency of T cell antigens is influenced by the formation of the immunological synapse. Immunity 26, 345–355 (2007).
von Boehmer, H. Unique features of the pre-T-cell receptor α-chain: not just a surrogate. Nat. Rev. Immunol. 5, 571–577 (2005).
Maillard, I., Fang, T. & Pear, W.S. Regulation of lymphoid development, differentiation, and function by the Notch pathway. Annu. Rev. Immunol. 23, 945–974 (2005).
Rothenberg, E.V., Moore, J.E. & Yui, M.A. Launching the T-cell-lineage developmental programme. Nat. Rev. Immunol. 8, 9–21 (2008).
Saint-Ruf, C. et al. Analysis and expression of a cloned pre-T cell receptor gene. Science 266, 1208–1212 (1994).
Fehling, H.J., Krotkova, A., Saint-Ruf, C. & von Boehmer, H. Crucial role of the pre-T-cell receptor α gene in development of αβ but not γδ T cells. Nature 375, 795–798 (1995).
Pang, S.S. et al. The structural basis for autonomous dimerization of the pre-T-cell antigen receptor. Nature 467, 844–848 (2010). This study reported a structure of the pre-TCRα paired with a TCRβ, providing a mechanistic explanation for the observed biology of the pre-TCR in β-selection.
Borowski, C., Li, X., Aifantis, I., Gounari, F. & von Boehmer, H. Pre-TCRα and TCRα are not interchangeable partners of TCRβ during T lymphocyte development. J. Exp. Med. 199, 607–615 (2004).
Ishikawa, E., Miyake, Y., Hara, H., Saito, T. & Yamasaki, S. Germ-line elimination of electric charge on pre-T-cell receptor (TCR) impairs autonomous signaling for β-selection and TCR repertoire formation. Proc. Natl. Acad. Sci. USA 107, 19979–19984 (2010).
Irving, B.A., Alt, F.W. & Killeen, N. Thymocyte development in the absence of pre-T cell receptor extracellular immunoglobulin domains. Science 280, 905–908 (1998).
Aifantis, I. et al. A critical role for the cytoplasmic tail of pTα in T lymphocyte development. Nat. Immunol. 3, 483–488 (2002).
Haks, M.C. et al. Low activation threshold as a mechanism for ligand-independent signaling in pre-T cells. J. Immunol. 170, 2853–2861 (2003).
Yamasaki, S. et al. Mechanistic basis of pre-T cell receptor-mediated autonomous signaling critical for thymocyte development. Nat. Immunol. 7, 67–75 (2006).
Li, Q.J. et al. miR-181a is an intrinsic modulator of T cell sensitivity and selection. Immunity 129, 147–161 (2007). This study described an additional role for microRNA in modulating TCR signaling capacity during thymocyte development through regulation of expression of signaling components, particularly inhibitory phosphatases.
Kisielow, P., Teh, H.S., Bluthmann, H. & von Boehmer, H. Positive selection of antigen-specific T cells in thymus by restricting MHC molecules. Nature 335, 730–733 (1988). This study provided the first evidence that positive selection is mediated by TCR recognition of MHC.
Teh, H.S. et al. Thymic major histocompatibility complex antigens and the αβ T-cell receptor determine the CD4/CD8 phenotype of T cells. Nature 335, 229–233 (1988).
Finkel, T.H. et al. The thymus has two functionally distinct populations of immature αβ+ T cells: one population is deleted by ligation of αβ TCR. Cell 58, 1047–1054 (1989).
Berg, L.J. et al. Antigen/MHC-specific T cells are preferentially exported from the thymus in the presence of their MHC ligand. Cell 58, 1035–1046 (1989).
Alam, S.M. et al. T-cell-receptor affinity and thymocyte positive selection. Nature 381, 616–620 (1996).
Williams, C.B., Engle, D.L., Kersh, G.J., Michael White, J. & Allen, P.M. A kinetic threshold between negative and positive selection based on the longevity of the T cell receptor-ligand complex. J. Exp. Med. 189, 1531–1544 (1999).
Kersh, G.J., Engle, D.L., Williams, C.B. & Allen, P.M. Ligand-specific selection of MHC class II-restricted thymocytes in fetal thymic organ culture. J. Immunol. 164, 5675–5682 (2000).
Naeher, D. et al. A constant affinity threshold for T cell tolerance. J. Exp. Med. 204, 2553–2559 (2007).
Ignatowicz, L., Kappler, J. & Marrack, P. The repertoire of T cells shaped by a single MHC/peptide ligand. Cell 84, 521–529 (1996). References 76 and 77 describe the ability of a single positively selecting pMHC ligand to generate a diverse T cell repertoire that can recognize a wide range of antigens.
Wang, B. et al. A single peptide-MHC complex positively selects a diverse and specific CD8 T cell repertoire. Science 326, 871–874 (2009).
Davey, G.M. et al. Preselection thymocytes are more sensitive to T cell receptor stimulation than mature T cells. J. Exp. Med. 188, 1867–1874 (1998).
Pircher, H., Rohrer, U.H., Moskophidis, D., Zinkernagel, R.M. & Hengartner, H. Lower receptor avidity required for thymic clonal deletion than for effector T-cell function. Nature 351, 482–485 (1991).
Werlen, G., Hausmann, B. & Palmer, E. A motif in the αβ T-cell receptor controls positive selection by modulating ERK activity. Nature 406, 422–426 (2000).
Mariathasan, S. et al. Duration and strength of extracellular signal-regulated kinase signals are altered during positive versus negative thymocyte selection. J. Immunol. 167, 4966–4973 (2001).
McNeil, L.K., Starr, T.K. & Hogquist, K.A. A requirement for sustained ERK signaling during thymocyte positive selection in vivo. Proc. Natl. Acad. Sci. USA 102, 13574–13579 (2005).
Fu, G. et al. Themis controls thymocyte selection through regulation of T cell antigen receptor-mediated signaling. Nat. Immunol. 10, 848–856 (2009).
Johnson, A.L. et al. Themis is a member of a new metazoan gene family and is required for the completion of thymocyte positive selection. Nat. Immunol. 10, 831–839 (2009).
Lesourne, R. et al. Themis, a T cell-specific protein important for late thymocyte development. Nat. Immunol. 10, 840–847 (2009).
Singer, A. & Bosselut, R. CD4/CD8 coreceptors in thymocyte development, selection, and lineage commitment: analysis of the CD4/CD8 lineage decision. Adv. Immunol. 83, 91–131 (2004).
Fischer, A.M., Katayama, C.D., Pages, G., Pouyssegur, J. & Hedrick, S.M. The role of Erk1 and Erk2 in multiple stages of T cell development. Immunity 23, 431–443 (2005).
Jordan, M.S. et al. Thymic selection of CD4+CD25+ regulatory T cells induced by an agonist self-peptide. Nat. Immunol. 2, 301–306 (2001).
Hsieh, C.S., Zheng, Y., Liang, Y., Fontenot, J.D. & Rudensky, A.Y. An intersection between the self-reactive regulatory and nonregulatory T cell receptor repertoires. Nat. Immunol. 7, 401–410 (2006).
Moran, A.E. et al. T cell receptor signal strength in Treg and iNKT cell development demonstrated by a novel fluorescent reporter mouse. J. Exp. Med. 208, 1279–1289 (2011).
Lio, C.W. & Hsieh, C.S. A two-step process for thymic regulatory T cell development. Immunity 28, 100–111 (2008).
Metzger, T.C. & Anderson, M.S. Control of central and peripheral tolerance by Aire. Immunol. Rev. 241, 89–103 (2011).
Gallegos, A.M. & Bevan, M.J. Central tolerance to tissue-specific antigens mediated by direct and indirect antigen presentation. J. Exp. Med. 200, 1039–1049 (2004).
Bommhardt, U., Scheuring, Y., Bickel, C., Zamoyska, R. & Hunig, T. MEK activity regulates negative selection of immature CD4+CD8+ thymocytes. J. Immunol. 164, 2326–2337 (2000).
Mallaun, M., Zenke, G. & Palmer, E. A discrete affinity-driven elevation of ZAP-70 kinase activity initiates negative selection. J. Recept. Signal Transduct. Res. 30, 430–443 (2010).
Filbert, E.L. et al. Kinase suppressor of Ras 1 is required for full ERK activation in thymocytes but not for thymocyte selection. Eur. J. Immunol. 40, 3226–3234 (2010).
Surh, C.D. & Sprent, J. Homeostasis of naive and memory T cells. Immunity 29, 848–862 (2008).
Takada, K. & Jameson, S.C. Naive T cell homeostasis: from awareness of space to a sense of place. Nat. Rev. Immunol. 9, 823–832 (2009).
Takeda, S., Rodewald, H.R., Arakawa, H., Bluethmann, H. & Shimizu, T. MHC class II molecules are not required for survival of newly generated CD4+ T cells, but affect their long-term life span. Immunity 5, 217–228 (1996).
Tanchot, C., Lemonnier, F.A., Perarnau, B., Freitas, A.A. & Rocha, B. Differential requirements for survival and proliferation of CD8 naive or memory T cells. Science 276, 2057–2062 (1997).
Ernst, B., Lee, D.S., Chang, J.M., Sprent, J. & Surh, C.D. The peptide ligands mediating positive selection in the thymus control T cell survival and homeostatic proliferation in the periphery. Immunity 11, 173–181 (1999).
Viret, C., Wong, F.S. & Janeway, C.A. Jr. Designing and maintaining the mature TCR repertoire: the continuum of self-peptide:self-MHC complex recognition. Immunity 10, 559–568 (1999).
Goldrath, A.W. & Bevan, M.J. Low-affinity ligands for the TCR drive proliferation of mature CD8+ T cells in lymphopenic hosts. Immunity 11, 183–190 (1999). References 101–103 identify the self-pMHCs important for T cell homeostasis in the periphery as the same self-ligands required for positive selection.
Goldrath, A.W., Hogquist, K.A. & Bevan, M.J. CD8 lineage commitment in the absence of CD8. Immunity 6, 633–642 (1997).
Kassiotis, G., Zamoyska, R. & Stockinger, B. Involvement of avidity for major histocompatibility complex in homeostasis of naive and memory T cells. J. Exp. Med. 197, 1007–1016 (2003).
Kieper, W.C., Burghardt, J.T. & Surh, C.D. A role for TCR affinity in regulating naive T cell homeostasis. J. Immunol. 172, 40–44 (2004).
Tarakhovsky, A. et al. A role for CD5 in TCR-mediated signal transduction and thymocyte selection. Science 269, 535–537 (1995).
Smith, K. et al. Sensory adaptation in naive peripheral CD4 T cells. J. Exp. Med. 194, 1253–1261 (2001).
Azzam, H.S. et al. CD5 expression is developmentally regulated by T cell receptor (TCR) signals and TCR avidity. J. Exp. Med. 188, 2301–2311 (1998).
Palmer, M.J., Mahajan, V.S., Chen, J., Irvine, D.J. & Lauffenburger, D.A. Signaling thresholds govern heterogeneity in IL-7-receptor-mediated responses of naive CD8+ T cells. Immunol. Cell Biol. 89, 581–594 (2011).
Ge, Q., Bai, A., Jones, B., Eisen, H.N. & Chen, J. Competition for self-peptide-MHC complexes and cytokines between naive and memory CD8+ T cells expressing the same or different T cell receptors. Proc. Natl. Acad. Sci. USA 101, 3041–3046 (2004).
Park, J.H. et al. ′Coreceptor tuning': cytokine signals transcriptionally tailor CD8 coreceptor expression to the self-specificity of the TCR. Nat. Immunol. 8, 1049–1059 (2007).
Casrouge, A. et al. Size estimate of the αβ TCR repertoire of naive mouse splenocytes. J. Immunol. 164, 5782–5787 (2000).
Robins, H.S. et al. Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells. Blood 114, 4099–4107 (2009).
Harding, C.V. & Unanue, E.R. Quantitation of antigen-presenting cell MHC class II/peptide complexes necessary for T-cell stimulation. Nature 346, 574–576 (1990).
Sykulev, Y., Joo, M., Vturina, I., Tsomides, T.J. & Eisen, H.N. Evidence that a single peptide-MHC complex on a target cell can elicit a cytolytic T cell response. Immunity 4, 565–571 (1996).
Irvine, D.J., Purbhoo, M.A., Krogsgaard, M. & Davis, M.M. Direct observation of ligand recognition by T cells. Nature 419, 845–849 (2002).
Luescher, I.F. et al. CD8 modulation of T-cell antigen receptor-ligand interactions on living cytotoxic T lymphocytes. Nature 373, 353–356 (1995).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Rights and permissions
About this article
Cite this article
Morris, G., Allen, P. How the TCR balances sensitivity and specificity for the recognition of self and pathogens. Nat Immunol 13, 121–128 (2012). https://doi.org/10.1038/ni.2190
Published:
Issue Date:
DOI: https://doi.org/10.1038/ni.2190