Making sense of mass destruction: quantitating MHC class I antigen presentation

Key Points

  • MHC class I molecules present peptide fragments mostly from nuclear and cytosolic antigens. Although the process is reasonably well characterized, the origin and whereabouts of the peptides has only recently become clear.

  • The latest additions to the scheme are peptidases. Various cytosolic aminopeptidases and an endoplasmic reticulum (ER) aminopeptidase have been defined. The half-life of peptides (5 seconds) in living cells has been determined.

  • Peptides can be derived not only from old proteins, but also from the same proteins that are degraded almost immediately after generation. This can be the result of defects in translation, folding or assembly, and the products are collectively known as defective ribosomal products (DRiPs). DRiPs are important to allow a rapid CD8+ T-cell response after infection.

  • Contrary to intuition, the process of antigen processing and presentation is inefficient. Potential antigens are destroyed at various levels including the proteasome, cytosolic peptidases and ER peptidases. The result of these processes is that only about one peptide out of every 10,000 proteins degraded will be presented by MHC class I molecules.

  • Many estimates have been made for the activities of the different steps in MHC class-I-antigen presentation. These numbers explain the inefficiency of MHC class-I-antigen presentation.

  • The inefficiency of antigen presentation sets a threshold on the minimum number of protein copies expressed for recognition by CD8+ T cells.

Abstract

MHC class I molecules bind short peptides and present them to CD8+ T cells. Contrary to textbook descriptions, the generation of MHC class-I-associated peptides from endogenous proteins is a highly dynamic and remarkably inefficient process. Here, we describe recent experiments that show how nascent and mature proteins are degraded into peptides that are trimmed, transported and trimmed again to enable presentation of a small portion of the generated peptides. By linking the failure rate of protein synthesis with antigen presentation, a rapid T-cell response is ensured, which is crucial in combating viral infections. Presentation on MHC class I molecules is achieved by less than 0.1% of the specific peptides that have survived intracellular destruction. The other peptides are converted into free amino acids that are used for recycling into new proteins.

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Figure 1: MHC class I antigen presentation: the basics.
Figure 2: The perils of protein biogenesis.
Figure 3: Complexities of MHC class I antigen presentation.
Figure 4: New economy of the various steps in MHC class I antigen processing per cell.

References

  1. 1

    Garboczi, D. N. et al. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature 384, 134–141 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2

    Garcia, K. C. et al. An αβ T cell receptor structure at 2. 5 Å and its orientation in the TCR–MHC complex. Science 274, 209–219 (1996).

    CAS  Article  Google Scholar 

  3. 3

    Falk, K., Rotzschke, O., Stevanovic, S., Jung, G. & Rammensee, H. G. Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351, 290–296 (1991).

    CAS  Google Scholar 

  4. 4

    Rock, K. L. et al. Inhibitors of the proteasome block the degradation of most cell proteins and the generation of peptides presented on MHC class I molecules. Cell 78, 761–771 (1994).

    CAS  Google Scholar 

  5. 5

    Reits, E. A., Benham, A. M., Plougastel, B., Neefjes, J. & Trowsdale, J. Dynamics of proteasome distribution in living cells. EMBO J. 16, 6087–6094 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. 6

    Kisselev, A. F., Akopian, T. N., Woo, K. M. & Goldberg, A. L. The sizes of peptides generated from protein by mammalian 26 and 20 S proteasomes. Implications for understanding the degradative mechanism and antigen presentation. J. Biol. Chem. 274, 3363–3371 (1999). This paper identifies the peptides that are generated by the proteasome under in vitro conditions. Only a small fraction of all peptides that are released by the proteasomes can bind directly with high affinity to MHC class I molecules. A marked fraction of peptides are too short for transport by transporter for antigen processing (TAP) and binding to MHC class I molecules.

    CAS  PubMed  PubMed Central  Google Scholar 

  7. 7

    Reits, E. et al. Peptide diffusion, protection, and degradation in nuclear and cytoplasmic compartments before antigen presentation by MHC class I. Immunity 18, 97–108 (2003). This report describes the fate of peptides in living cells. Using bleaching techniques, it is shown that peptides associate with chromatin. However, peptides have to leave the nucleus to contact TAP and are rapidly degraded in the cytoplasm by resident peptidases. As a result, more than 99% will not reach TAP for translocation into the endoplasmic reticulum (ER).

    CAS  PubMed  PubMed Central  Google Scholar 

  8. 8

    Serwold, T., Gonzalez, F., Kim, J., Jacob, R. & Shastri, N. ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum. Nature 419, 480–483 (2002).

    CAS  Google Scholar 

  9. 9

    Saric, T. et al. An IFN-γ-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I-presented peptides. Nature Immunol. 3, 1169–1176 (2002).

    CAS  Google Scholar 

  10. 10

    Neefjes, J. J., Momburg, F. & Hammerling, G. J. Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter. Science 261, 769–771 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. 11

    van Endert, P. M., Saveanu, L., Hewitt, E. W. & Lehner, P. Powering the peptide pump: TAP crosstalk with energetic nucleotides. Trends Biochem. Sci. 27, 454–461 (2002).

    CAS  PubMed  Google Scholar 

  12. 12

    Ortmann, B. et al. A critical role for tapasin in the assembly and function of multimeric MHC class I–TAP complexes. Science 277, 1306–1309 (1997).

    CAS  Google Scholar 

  13. 13

    Garbi, N. et al. Impaired immune responses and altered peptide repertoire in tapasin-deficient mice. Nature Immunol. 1, 234–238 (2000).

    CAS  Google Scholar 

  14. 14

    Dick, T. P., Bangia, N., Peaper, D. R. & Cresswell, P. Disulfide bond isomerization and the assembly of MHC class I–peptide complexes. Immunity 16, 87–98 (2002).

    CAS  Google Scholar 

  15. 15

    Cascio, P., Hilton, C., Kisselev, A. F., Rock, K. L. & Goldberg, A. L. 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide. EMBO J. 20, 2357–2366 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  16. 16

    Momburg, F., Roelse, J., Hammerling, G. J. & Neefjes, J. J. Peptide size selection by the major histocompatibility complex-encoded peptide transporter. J. Exp. Med. 179, 1613–1623 (1994).

    CAS  PubMed  Google Scholar 

  17. 17

    Neisig, A., Wubbolts, R., Zang, X., Melief, C. & Neefjes, J. Allele-specific differences in the interaction of MHC class I molecules with transporters associated with antigen processing. J. Immunol. 156, 3196–3206 (1996).

    CAS  PubMed  Google Scholar 

  18. 18

    Zweerink, H. J. et al. Presentation of endogenous peptides to MHC class I-restricted cytotoxic T lymphocytes in transport deletion mutant T2 cells. J. Immunol. 150, 1763–1771 (1993).

    CAS  PubMed  Google Scholar 

  19. 19

    Wei, M. L. & Cresswell, P. HLA-A2 molecules in an antigen-processing mutant cell contain signal sequence-derived peptides. Nature 356, 443–446 (1992).

    CAS  PubMed  Google Scholar 

  20. 20

    Williams, D. B., Swiedler, S. J. & Hart, G. W. Intracellular transport of membrane glycoproteins: two closely related histocompatibility antigens differ in their rates of transit to the cell surface. J. Cell Biol. 101, 725–734 (1985).

    CAS  PubMed  Google Scholar 

  21. 21

    Neefjes, J. J. & Ploegh, H. L. Allele and locus-specific differences in cell surface expression and the association of HLA class I heavy chain with β2-microglobulin: differential effects of inhibition of glycosylation on class I subunit association. Eur. J. Immunol. 18, 801–810 (1988).

    CAS  PubMed  Google Scholar 

  22. 22

    Lammert, E., Stevanovic, S., Brunner, J., Rammensee, H. G. & Schild, H. Protein disulfide isomerase is the dominant acceptor for peptides translocated into the endoplasmic reticulum. Eur. J. Immunol. 27, 1685–1690 (1997).

    CAS  PubMed  Google Scholar 

  23. 23

    Spee, P. & Neefjes, J. TAP-translocated peptides specifically bind proteins in the endoplasmic reticulum, including gp96, protein disulfide isomerase and calreticulin. Eur. J. Immunol. 27, 2441–2449 (1997).

    CAS  Google Scholar 

  24. 24

    Koopmann, J. O. et al. Export of antigenic peptides from the endoplasmic reticulum intersects with retrograde protein translocation through the Sec61p channel. Immunity 13, 117–127 (2000).

    CAS  PubMed  Google Scholar 

  25. 25

    Roelse, J., Gromme, M., Momburg, F., Hammerling, G. & Neefjes, J. Trimming of TAP-translocated peptides in the endoplasmic reticulum and in the cytosol during recycling. J. Exp. Med. 180, 1591–1597 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26

    Seifert, U. et al. An essential role for tripeptidyl peptidase in the generation of an MHC class I epitope. Nature Immunol. 4, 375–379 (2003).

    CAS  Google Scholar 

  27. 27

    Glas, R., Bogyo, M., McMaster, J. S., Gaczynska, M. & Ploegh, H. L. A proteolytic system that compensates for loss of proteasome function. Nature 392, 618–622 (1998).

    CAS  PubMed  Google Scholar 

  28. 28

    Princiotta, M. F. et al. Cells adapted to the proteasome inhibitor 4-hydroxy-5-iodo-3-nitrophenylacetyl-Leu-Leu-leucinal-vinyl sulfone require enzymatically active proteasomes for continued survival. Proc. Natl Acad. Sci. USA 98, 513–518 (2001).

    CAS  PubMed  Google Scholar 

  29. 29

    Gromme, M. et al. Recycling MHC class I molecules and endosomal peptide loading. Proc. Natl Acad. Sci. USA 96, 10326–10331 (1999).

    CAS  PubMed  Google Scholar 

  30. 30

    Kleijmeer, M. J. et al. Antigen loading of MHC class I molecules in the endocytic tract. Traffic 2, 124–137 (2001).

    CAS  PubMed  Google Scholar 

  31. 31

    Jackson, P. K. et al. The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases. Trends Cell Biol. 10, 429–439 (2000).

    CAS  Google Scholar 

  32. 32

    Glickman, M. H. & Ciechanover, A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol. Rev. 82, 373–428 (2002).

    CAS  Google Scholar 

  33. 33

    Navon, A. & Goldberg, A. L. Proteins are unfolded on the surface of the ATPase ring before transport into the proteasome. Mol. Cell 8, 1339–1349 (2001).

    CAS  PubMed  Google Scholar 

  34. 34

    Benaroudj, N., Zwickl, P., Seemuller, E., Baumeister, W. & Goldberg, A. L. ATP hydrolysis by the proteasome regulatory complex PAN serves multiple functions in protein degradation. Mol. Cell 11, 69–78 (2003).

    CAS  Article  Google Scholar 

  35. 35

    Ogura, T. & Tanaka, K. Dissecting various ATP-dependent steps involved in proteasomal degradation. Mol. Cell 11, 3–5 (2003).

    CAS  PubMed  Google Scholar 

  36. 36

    Kloetzel, P. M. Antigen processing by the proteasome. Nature Rev. Mol. Cell Biol. 2, 179–187 (2001).

    CAS  Google Scholar 

  37. 37

    York, I. A. et al. The cytosolic endopeptidase, thimet oligopeptidase, destroys antigenic peptides and limits the extent of MHC class I antigen presentation. Immunity 18, 429–440 (2003). This paper, together with reference 39, provides examples of various peptidases that either generate or destroy peptides for MHC class I antigen presentation. This depends on peptide size and sequence.

    CAS  Google Scholar 

  38. 38

    Stoltze, L. et al. Two new proteases in the MHC class I processing pathway. Nature Immunol. 1, 413–418 (2000).

    CAS  Google Scholar 

  39. 39

    York, I. A. et al. The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8–9 residues. Nature Immunol. 3, 1177–1184 (2002).

    CAS  Google Scholar 

  40. 40

    Neisig, A. et al. Major differences in transporter associated with antigen presentation (TAP)-dependent translocation of MHC class I-presentable peptides and the effect of flanking sequences. J. Immunol. 154, 1273–1279 (1995).

    CAS  Google Scholar 

  41. 41

    De Plaen, E. et al. Immunogenic (tum-) variants of mouse tumor P815: cloning of the gene of tum-antigen P91A and identification of the tum-mutation. Proc. Natl Acad. Sci. USA 85, 2274–2278 (1988).

    CAS  PubMed  Google Scholar 

  42. 42

    Schwab, S. R., Li, K. C., Kang, C. & Shastri, N. Constitutive display of cryptic translation products by MHC class I molecules. Science 301, 1367–1371 (2003).

    CAS  PubMed  Google Scholar 

  43. 43

    Yewdell, J. W., Anton, L. C. & Bennink, J. R. Defective ribosomal products (DRiPs): a major source of antigenic peptides for MHC class I molecules? J. Immunol. 157, 1823–1826 (1996). The first paper to describe the concept of defective ribosomal products (DRiPs).

    CAS  PubMed  Google Scholar 

  44. 44

    Bach, I. & Ostendorff, H. P. Orchestrating nuclear functions: ubiquitin sets the rhythm. Trends Biochem. Sci. 28, 189–195 (2003).

    CAS  PubMed  Google Scholar 

  45. 45

    Jackson, P. K. & Eldridge, A. G. The SCF ubiquitin ligase: an extended look. Mol. Cell 9, 923–925 (2002).

    CAS  PubMed  Google Scholar 

  46. 46

    Schimke, R. T. & Doyle, D. Control of enzyme levels in animal tissues. Annu. Rev. Biochem. 39, 929–976 (1970).

    CAS  PubMed  Google Scholar 

  47. 47

    Goldberg, A. Intracellular protein degradation in mammalian and bacterial cells. Annu. Rev. Biochem. 45, 747–803 (1976).

    CAS  PubMed  Google Scholar 

  48. 48

    Yewdell, J. W. Not such a dismal science: the economics of protein synthesis, folding, degradation and antigen processing. Trends Cell Biol. 11, 294–297 (2001).

    CAS  Google Scholar 

  49. 49

    Yewdell, J. W., Schubert, U. & Bennink, J. R. At the crossroads of cell biology and immunology: DRiPs and other sources of peptide ligands for MHC class I molecules. J. Cell Sci. 114, 845–851 (2001).

    CAS  PubMed  Google Scholar 

  50. 50

    Esquivel, F., Yewdell, J. & Bennink, J. RMA/S cells present endogenously synthesized cytosolic proteins to class I-restricted cytotoxic T lymphocytes. J. Exp. Med. 175, 163–168 (1992).

    CAS  PubMed  Google Scholar 

  51. 51

    Khan, S. et al. Cutting edge: neosynthesis is required for the presentation of a T cell epitope from a long-lived viral protein. J. Immunol. 167, 4801–4804 (2001). References 51, 52 and 56 provide biochemical, cell biological and immunological evidence for the DRiP hypothesis. They imply that protein generation is tightly linked to antigen presentation by MHC class I molecules.

    CAS  PubMed  Google Scholar 

  52. 52

    Reits, E. A., Vos, J. C., Gromme, M. & Neefjes, J. The major substrates for TAP in vivo are derived from newly synthesized proteins. Nature 404, 774–778 (2000).

    CAS  PubMed  Google Scholar 

  53. 53

    Schild, H. & Rammensee, H. G. Perfect use of imperfection. Nature 404, 709–710 (2000).

    CAS  PubMed  Google Scholar 

  54. 54

    Wheatley, D. N. & Inglis, M. S. Turnover of nascent proteins in HeLa-S3 cells and the quasi-linear incorporation kinetics of amino acids. Cell Biol. Int. Rep. 9, 463–470 (1985).

    CAS  PubMed  Google Scholar 

  55. 55

    Wheatley, D. N. Protein turnover in relation to growth status and the cell cycle in cultured mammalian cells. Revis. Biol. Cellular 21, 377–400 (1989).

    CAS  Google Scholar 

  56. 56

    Schubert, U. et al. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature 404, 770–774 (2000).

    CAS  Google Scholar 

  57. 57

    Turner, G. C. & Varshavsky, A. Detecting and measuring cotranslational protein degradation in vivo. Science 289, 2117–2120 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Jensen, T. J. et al. Multiple proteolytic systems, including the proteasome, contribute to CFTR processing. Cell 83, 129–135 (1995).

    CAS  PubMed  Google Scholar 

  59. 59

    Ward, C. L., Omura, S. & Kopito, R. R. Degradation of CFTR by the ubiquitin-proteasome pathway. Cell 83, 121–127 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. 60

    Pareek, S. et al. Neurons promote the translocation of peripheral myelin protein 22 into myelin. J. Neurosci. 17, 7754–7762 (1997).

    CAS  PubMed  Google Scholar 

  61. 61

    Notterpek, L., Ryan, M. C., Tobler, A. R. & Shooter, E. M. PMP22 accumulation in aggresomes: implications for CMT1A pathology. Neurobiol. Dis. 6, 450–460 (1999).

    CAS  PubMed  Google Scholar 

  62. 62

    Siffroi-Fernandez, S., Giraud, A., Lanet, J. & Franc, J. L. Association of the thyrotropin receptor with calnexin, calreticulin and BiP. Efects on the maturation of the receptor. Eur. J. Biochem. 269, 4930–4937 (2002).

    CAS  PubMed  Google Scholar 

  63. 63

    Petaja-Repo, U. E. et al. Newly synthesized human δ-opioid receptors retained in the endoplasmic reticulum are retrotranslocated to the cytosol, deglycosylated, ubiquitinated, and degraded by the proteasome. J. Biol. Chem. 276, 4416–4423 (2001).

    CAS  PubMed  Google Scholar 

  64. 64

    Yedidia, Y., Horonchik, L., Tzaban, S., Yanai, A. & Taraboulos, A. Proteasomes and ubiquitin are involved in the turnover of the wild-type prion protein. EMBO J. 20, 5383–5391 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65

    Drisaldi, B. et al. Mutant PrP is delayed in its exit from the endoplasmic reticulum, but neither wild-type nor mutant PrP undergoes retrotranslocation prior to proteasomal degradation. J. Biol. Chem. 278, 21732–21743 (2003).

    CAS  Google Scholar 

  66. 66

    Princiotta, M. F. et al. Quantitating protein synthesis, degradation, and endogenous antigen processing. Immunity 18, 343–354 (2003). This paper shows the full quantification of the steps between protein synthesis and MHC class I antigen presentation. It visualizes the impact of DRiPs on MHC class-I-associated peptides.

    CAS  Google Scholar 

  67. 67

    Kenniston, J. A., Baker, T. A., Fernandez, J. M. & Sauer, R. T. Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine. Cell 114, 511–520 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68

    Verma, R. & Deshaies, R. J. A proteasome howdunit: the case of the missing signal. Cell 101, 341–344 (2000).

    CAS  Google Scholar 

  69. 69

    Dantuma, N. P., Lindsten, K., Glas, R., Jellne, M. & Masucci, M. G. Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. Nature Biotechnol. 18, 538–543 (2000).

    CAS  Google Scholar 

  70. 70

    Bence, N. F., Sampat, R. M. & Kopito, R. R. Impairment of the ubiquitin-proteasome system by protein aggregation. Science 292, 1552–1555 (2001).

    CAS  Google Scholar 

  71. 71

    Falk, K., Rotzschke, O. & Rammensee, H. G. Cellular peptide composition governed by major histocompatibility complex class I molecules. Nature 348, 248–251 (1990).

    CAS  Google Scholar 

  72. 72

    Porgador, A., Yewdell, J. W., Deng, Y., Bennink, J. R. & Germain, R. N. Localization, quantitation, and in situ detection of specific peptide–MHC class I complexes using a monoclonal antibody. Immunity 6, 715–726 (1997).

    CAS  Google Scholar 

  73. 73

    Benham, A. M. & Neefjes, J. J. Proteasome activity limits the assembly of MHC class I molecules after IFN-γ stimulation. J. Immunol. 159, 5896–5904 (1997).

    CAS  PubMed  Google Scholar 

  74. 74

    Anton, L. C. et al. Dissociation of proteasomal degradation of biosynthesized viral proteins from generation of MHC class I-associated antigenic peptides. J. Immunol. 160, 4859–4868 (1998).

    CAS  PubMed  Google Scholar 

  75. 75

    Ben-Shahar, S. et al. 26 S proteasome-mediated production of an authentic major histocompatibility class I-restricted epitope from an intact protein substrate. J. Biol. Chem. 274, 21963–21972 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. 76

    Fruci, D. et al. Quantifying recruitment of cytosolic peptides for HLA class I presentation: impact of TAP transport. J. Immunol. 170, 2977–2984 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77

    Villanueva, M. S., Fischer, P., Feen, K. & Pamer, E. G. Efficiency of MHC class I antigen processing: a quantitative analysis. Immunity 1, 479–489 (1994).

    CAS  PubMed  Google Scholar 

  78. 78

    Guermonprez, P. et al. ER–phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells. Nature 425, 397–402 (2003).

    CAS  PubMed  Google Scholar 

  79. 79

    Houde, M. et al. Phagosomes are competent organelles for antigen cross-presentation. Nature 425, 402–406 (2003).

    CAS  PubMed  Google Scholar 

  80. 80

    Denkberg, G. et al. Direct visualization of distinct T cell epitopes derived from a melanoma tumor-associated antigen by using human recombinant antibodies with MHC-restricted T cell receptor-like specificity. Proc. Natl Acad. Sci. USA 99, 9421–9426 (2002).

    CAS  PubMed  Google Scholar 

  81. 81

    Jardetzky, T. S., Lane, W. S., Robinson, R. A., Madden, D. R. & Wiley, D. C. Identification of self peptides bound to purified HLA-B27. Nature 353, 326–329 (1991).

    CAS  PubMed  Google Scholar 

  82. 82

    Admon, A., Barnea, E. & Ziv, T. Tumor antigens and proteomics from the point of view of the major histocompatibility complex peptides. Mol. Cell. Proteomics 2, 388–398 (2003).

    CAS  PubMed  Google Scholar 

  83. 83

    Turzynski, A. & Mentlein, R. Prolyl aminopeptidase from rat brain and kidney. Action on peptides and identification as leucyl aminopeptidase. Eur. J. Biochem. 190, 509–515 (1990).

    CAS  PubMed  Google Scholar 

  84. 84

    Beninga, J., Rock, K. L. & Goldberg, A. L. Interferon-γ can stimulate post-proteasomal trimming of the N terminus of an antigenic peptide by inducing leucine aminopeptidase. J. Biol. Chem. 273, 18734–18742 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. 85

    Geier, E. et al. A giant protease with potential to substitute for some functions of the proteasome. Science 283, 978–981 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. 86

    Macpherson, E., Tomkinson, B., Balow, R. M., Hoglund, S. & Zetterqvist, O. Supramolecular structure of tripeptidyl peptidase II from human erythrocytes as studied by electron microscopy, and its correlation to enzyme activity. Biochem. J. 248, 259–263 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87

    Tomkinson, B. Tripeptidyl peptidases: enzymes that count. Trends Biochem. Sci. 24, 355–359 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    Saric, T. et al. Major histocompatibility complex class I-presented antigenic peptides are degraded in cytosolic extracts primarily by thimet oligopeptidase. J. Biol. Chem. 276, 36474–36481 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. 89

    Bromme, D., Rossi, A. B., Smeekens, S. P., Anderson, D. C. & Payan, D. G. Human bleomycin hydrolase: molecular cloning, sequencing, functional expression, and enzymatic characterization. Biochemistry 35, 6706–6714 (1996).

    CAS  PubMed  Google Scholar 

  90. 90

    Johnson, G. D. & Hersh, L. B. Studies on the subsite specificity of the rat brain puromycin-sensitive aminopeptidase. Arch. Biochem. Biophys. 276, 305–309 (1990).

    CAS  PubMed  Google Scholar 

  91. 91

    Gakamsky, D. M., Davis, D. M., Strominger, J. L. & Pecht, I. Assembly and dissociation of human leukocyte antigen (HLA)-A2 studied by real-time fluorescence resonance energy transfer. Biochemistry 39, 11163–11169 (2000).

    CAS  PubMed  Google Scholar 

  92. 92

    Thulasiraman, V., Yang, C. F. & Frydman, J. In vivo newly translated polypeptides are sequestered in a protected folding environment. EMBO J. 18, 85–95 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

We thank C. Sanders at Vanderbilt University for providing examples of inefficient protein biogenesis. This work was supported by the Dutch Cancer Society KWF.

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Correspondence to Jacques Neefjes.

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Supplementary information

Cartoon 1 | MHC class I antigen presentation: the basics. Intracellular proteins are degraded by the proteasome into peptides. The transporter for antigen processing (TAP) then translocates peptides into the lumen of the endoplasmic reticulum (ER). Newly synthesized MHC class I molecules require peptide binding for release from the ER and transport to the plasma membrane, where the peptide is presented to the immune system. (JPG 72 kb)

Cartoon 2 | The perils of protein biogenesis. All proteins are made by the ribosome using messenger RNA as a template. Nascent proteins are frequently stabilized by heat-shock proteins (HSPs), which probably facilitate correct folding and prevent aggregation. Despite this, a marked fraction of translation products is defective, resulting in incorrect (mistranslated or prematurely stopped), misfolded or misassembled proteins. These defective ribosomal products (DRiPs) are shunted to the proteasome for degradation, coupling protein production to MHC class I antigen presentation and enable a rapid T-cell response to new viral proteins. (JPG 84 kb)

Cartoon 3 | Complexities of MHC class I antigen presentation. Both defective ribosomal products (DRiPs) and mature proteins (retirees) are degraded by proteasomes, usually after polyubiquitylation. The proteasome digests proteins into peptides of various lengths. Many peptides are too small for presentation by MHC class I molecules and are recycled into amino acids that can be used for new proteins. Another fraction is appropriate or too long for MHC class I molecules. These, too, are substrates for various cytosolic peptidases that will degrade most to amino acids. Only a few (trimmed) peptides diffuse into the transporter for antigen processing (TAP). TAP translocates peptides into the lumen of the endoplasmic reticulum (ER), where they can associate with MHC class I molecules before or after trimming by ER aminopeptidases (ERAP). Peptides that fail to bind to MHC class I molecules are removed by the translocon SEC61 and enter the cytoplasm, where they will again be targets for the cytosolic peptidases. (JPG 137 kb)

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Glossary

SIGNAL PEPTIDES

Targeting sequences in proteins that are required to send them to their subsequent destination. This could be the mitochondrion, nucleus, peroxisome or ER, endoplasmic reticulum, depending on amino-acid sequence and positioning in the protein. Signal sequences for ER targeting enter the ER lumen, are cleaved off, and can end up as an MHC class-I-binding peptide.

ERAP1

This endoplasmic-reticulum-resident aminopeptidase trims peptides to the size that is suitable for binding to MHC class I molecules. As both the proteasome and transporter for antigen processing handle peptides that are longer than those that bind to MHC class I molecules, either cytosolic peptidases and/or ERAP1 are required for correct epitope generation.

SEC61 TRANSLOCON

An endoplasmic reticulum (ER) complex used by the ribosome to transfer nascent proteins into the ER lumen during translation. The same complex is also used to remove ER proteins and peptides, for transfer in the ER and degradation by the proteasome and peptidases, respectively.

CROSS-PRIMING

Initiation of a CD8+ T-cell response to an antigen that is not present in antigen-presenting cells (APCs). The antigen must be taken up by APCs and then re-routed to the MHC class-I-presentation pathway.

DEFECTIVE RIBOSOMAL PRODUCTS

(DRiPs). DRiPs include all proteins that are degraded by the proteasome before becoming functional. This could be the result of defects in transcription, splicing, translation, assembly or folding. DRiPs link antigen generation to presentation and ensure rapid CD8+ T-cell responses to infections.

F-BOX PROTEINS

The target-recognizing subunit of the SCF (SKP1–cullin–F-box) complex. About 70 different F-box proteins are encoded in the human genome, most with unknown substrate specificity. After recognition by the F-box protein, E2 ubiquitin ligase transfers the first ubiquitin tag to the target protein, thereby initiating poly-ubiquitylation and ultimately degradation by the proteasome.

FLUORESCENCE LOSS IN PHOTOBLEACHING

(FLIP). FLIP is the reverse of FRAP (fluorescence recovery after photobleaching) and is a microscopy technique used to follow the dynamics of fluorescent molecules in living cells. By bleaching fluorescence at one site in a cell, the redistribution of fluorescence to other sites illustrates the dynamics of the fluorescent probes.

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Yewdell, J., Reits, E. & Neefjes, J. Making sense of mass destruction: quantitating MHC class I antigen presentation. Nat Rev Immunol 3, 952–961 (2003). https://doi.org/10.1038/nri1250

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