Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Post-proteasomal antigen processing for major histocompatibility complex class I presentation

Nature Immunology volume 5, pages 670–677 (2004)Cite this article

Abstract

Peptides presented by major histocompatibility complex class I molecules are derived mainly from cytosolic oligopeptides generated by proteasomes during the degradation of intracellular proteins. Proteasomal cleavages generate the final C terminus of these epitopes. Although proteasomes may produce mature epitopes that are eight to ten residues in length, they more often generate N-extended precursors that are too long to bind to major histocompatibility complex class I molecules. Such precursors are trimmed in the cytosol or in the endoplasmic reticulum by aminopeptidases that generate the N terminus of the presented epitope. Peptidases can also destroy epitopes by trimming peptides to below the size needed for presentation. In the cytosol, endopeptidases, especially thimet oligopeptidase, and aminopeptidases degrade many proteasomal products, thereby limiting the supply of many antigenic peptides. Thus, the extent of antigen presentation depends on the balance between several proteolytic processes that may generate or destroy epitopes.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Generation of the termini of MHC class I–binding peptides.
Figure 2: Proteasomes generate MHC class I–binding peptides inefficiently.
Figure 3: The size preference of ERAP1 leads to different effects on presentation by different MHC class I alleles.
Figure 4: MHC class I antigen presentation reflects a balance between destruction and production of peptides.

Similar content being viewed by others

References

  1. Rock, K.L. & Goldberg, A.L. Degradation of cell proteins and the generation of MHC class I-presented peptides. Annu. Rev. Immunol. 17, 739–779 (1999).

    Article  CAS  Google Scholar 

  2. York, I.A., Goldberg, A.L., Mo, X.Y. & Rock, K.L. Proteolysis and class I major histocompatibility complex antigen presentation. Immunol. Rev. 172, 49–66 (1999).

    Article  CAS  Google Scholar 

  3. Rock, K.L., York, I.A., Saric, T. & Goldberg, A.L. Protein degradation and the generation of MHC class I-presented peptides. Adv. Immunol. 80, 1–70 (2002).

    Article  CAS  Google Scholar 

  4. Shastri, N., Schwab, S. & Serwold, T. Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules. Annu. Rev. Immunol. 20, 463–493 (2002).

    Article  CAS  Google Scholar 

  5. Rammensee, H.G. Chemistry of peptides associated with MHC class I and class II molecules. Curr. Opin. Immunol. 7, 85–96 (1995).

    Article  CAS  Google Scholar 

  6. Princiotta, M.F. et al. Quantitating protein synthesis, degradation, and endogenous antigen processing. Immunity 18, 343–354 (2003).

    Article  CAS  Google Scholar 

  7. Goldberg, A.L., Cascio, P., Saric, T. & Rock, K.L. The importance of the proteasome and subsequent proteolytic steps in the generation of antigenic peptides. Mol. Immunol. 1169, 1–17 (2002).

    Google Scholar 

  8. Goldberg, A.L. Protein degradation and protection against misfolded or damaged proteins. Nature 426, 895–899 (2003).

    Article  CAS  Google Scholar 

  9. Kloetzel, P.-M. Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII. Nat. Immunol. 5, 661–669 (2004).

    Article  CAS  Google Scholar 

  10. 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).

    Article  CAS  Google Scholar 

  11. Craiu, A., Aklopian, T., Goldberg, A.L. & Rock, K.L. Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide. Proc. Natl. Acad. Sci. USA 94, 10850–10855 (1997).

    Article  CAS  Google Scholar 

  12. Cerundolo, V. et al. The proteasome-specific inhibitor lactacystin blocks presentation of cytotoxic T lymphocyte epitopes in human and murine cells. Eur. J. Immunol. 27, 336–341 (1997).

    Article  CAS  Google Scholar 

  13. Schwarz, K. et al. The selective proteasome inhibitors lactacystin and epoxomicin can be used to either up- or down-regulate antigen presentation at nontoxic doses. J. Immunol. 164, 6147–6157 (2000).

    Article  CAS  Google Scholar 

  14. Mo, X.Y., Cascio, P., Lemerise, K., Goldberg, A.L. & Rock, K. Distinct proteolytic processes generate the C and N termini of MHC class I-binding peptides. J. Immunol. 163, 5851–5859 (1999).

    CAS  Google Scholar 

  15. Stoltze, L. et al. Generation of the vesicular stomatitis virus nucleoprotein cytotoxic T lymphocyte epitope requires proteasome-dependent and -independent proteolytic activities. Eur. J. Immunol. 28, 4029–4036 (1998).

    Article  CAS  Google Scholar 

  16. 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).

    Article  CAS  Google Scholar 

  17. Toes, R.E. et al. Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products. J. Exp. Med. 194, 1–12 (2001).

    Article  CAS  Google Scholar 

  18. 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).

    Article  CAS  Google Scholar 

  19. Kessler, J.H. et al. Efficient identification of novel HLA-A*0201-presented cytotoxic T lymphocyte epitopes in the widely expressed tumor antigen PRAME by proteasome-mediated digestion analysis. J. Exp. Med. 193, 73–88 (2001).

    Article  CAS  Google Scholar 

  20. Morel, S. et al. Processing of some antigens by the standard proteasome but not by the immunoproteasome results in poor presentation by dendritic cells. Immunity 12, 107–117 (2000).

    Article  CAS  Google Scholar 

  21. Lucchiari-Hartz, M. et al. Cytotoxic T lymphocyte epitopes of HIV-1 Nef: Generation of multiple definitive major histocompatibility complex class I ligands by proteasomes. J. Exp. Med. 17, 239–252 (2000).

    Article  Google Scholar 

  22. 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).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  24. Reits, E. et al. A major role for TPPII in trimming proteasomal degradation products for MHC class I antigen presentation. Immunity 20, 495–506 (2004).

    Article  CAS  Google Scholar 

  25. Srivastava, P. Interaction of heat shock proteins with peptides and antigen presenting cells: chaperoning of the innate and adaptive immune responses. Annu. Rev. Immunol. 20, 395–425 (2002).

    Article  CAS  Google Scholar 

  26. Ishii, T. et al. Isolation of MHC class I-restricted tumor antigen peptide and its precursors associated with heat shock proteins hsp70, hsp90, and gp96. J. Immunol. 162, 1303–1309 (1999).

    CAS  Google Scholar 

  27. 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).

    Article  CAS  Google Scholar 

  28. 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).

    Article  CAS  Google Scholar 

  29. Lauvau, G. et al. Human transporters associated with antigen processing (TAPs) select epitope precursor peptides for processing in the endoplasmic reticulum and presentation to T cells. J. Exp. Med. 190, 1227–1240 (1999).

    Article  CAS  Google Scholar 

  30. Knuehl, C. et al. The murine cytomegalovirus pp89 immunodominant H-2Ld epitope is generated and translocated into the endoplasmic reticulum as an 11-mer precursor peptide. J. Immunol. 167, 1515–1521 (2001).

    Article  CAS  Google Scholar 

  31. 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 

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

    Article  CAS  Google Scholar 

  33. Elliott, T., Willis, A., Cerundolo, V. & Townsend, A. Processing of major histocompatibility class I-restricted antigens in the endoplasmic reticulum. J. Exp. Med. 181, 1481–1491 (1995).

    Article  CAS  Google Scholar 

  34. Lobigs, M., Chelvanayagam, G. & Mullbacher, A. Proteolytic processing of peptides in the lumen of the endoplasmic reticulum for antigen presentation by major histocompatibility class I. Eur. J. Immunol. 30, 1496–1506 (2000).

    Article  CAS  Google Scholar 

  35. Snyder, H.L., Yewdell, J.W. & Bennink, J.R. Trimming of antigenic peptides in an early secretory compartment. J. Exp. Med. 180, 2389–2394 (1994).

    Article  CAS  Google Scholar 

  36. 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).

    Article  CAS  Google Scholar 

  37. Paz, P., Brouwenstijn, N., Perry, R. & Shastri, N. Discrete proteolytic intermediates in the MHC class I antigen processing pathway and MHC I-dependent peptide trimming in the ER. Immunity 11, 241–251 (1999).

    Article  CAS  Google Scholar 

  38. Fruci, D., Niedermann, G., Butler, R.H. & van Endert, P.M. Efficient MHC class I-independent amino-terminal trimming of epitope precursor peptides in the endoplasmic reticulum. Immunity 15, 467–476 (2001).

    Article  CAS  Google Scholar 

  39. Anderson, K. et al. Endogenously synthesized peptide with an endoplasmic reticulum signal sequence sensitizes antigen processing mutant cells to class I-restricted cell-mediated lysis. J. Exp. Med. 174, 489–492 (1991).

    Article  CAS  Google Scholar 

  40. Wang, Y., Guttoh, D.S. & Androlewicz, M.J. TAP prefers to transport melanoma antigenic peptides which are longer than the optimal T-cell epitope: evidence for further processing in the endoplasmic reticulum. Melanoma Res. 8, 345–353 (1998).

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  42. Henderson, R.A. et al. HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation. Science 255, 1264–1266 (1992).

    Article  CAS  Google Scholar 

  43. Komlosh, A. et al. A role for a novel luminal endoplasmic reticulum aminopeptidase in final trimming of 26 S proteasome-generated major histocompatability complex class I antigenic peptides. J. Biol. Chem. 276, 30050–30056 (2001).

    Article  CAS  Google Scholar 

  44. Brouwenstijn, N., Serwold, T. & Shastri, N. MHC class I molecules can direct proteolytic cleavage of antigenic precursors in the endoplasmic reticulum. Immunity 15, 95–104 (2001).

    Article  CAS  Google Scholar 

  45. Serwold, T., Gaw, S. & Shastri, N. ER aminopeptidases generate a unique pool of peptides for MHC class I molecules. Nat. Immunol. 2, 644–651 (2001).

    Article  CAS  Google Scholar 

  46. 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).

    Article  CAS  Google Scholar 

  47. Hattori, A., Matsumoto, H., Mizutani, S. & Tsujimoto, M. Molecular cloning of adipocyte-derived leucine aminopeptidase highly related to placental leucine aminopeptidase/oxytocinase. J. Biochem. (Tokyo) 125, 931–938 (1999).

    Article  CAS  Google Scholar 

  48. Cui, X. et al. Identification of ARTS-1 as a novel TNFR1-binding protein that promotes TNFR1 ectodomain shedding. J. Clin. Invest. 110, 515–526 (2002).

    Article  CAS  Google Scholar 

  49. Schomburg, L., Kollmus, H., Friedrichsen, S. & Bauer, K. Molecular characterization of a puromycin-insensitive leucyl-specific aminopeptidase, PILS-AP. Eur. J. Biochem. 267, 3198–3207 (2000).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  51. Koopmann, J.O., Post, M., Neffjes, J.J., Hammerling, G.J. & Momburg, F. Translocation of long peptides by transporters associated with antigen processing (TAP). Eur. J. Immunol. 26, 1720–1728 (1996).

    Article  CAS  Google Scholar 

  52. Tanioka, T. et al. Human leukocyte-derived arginine aminopeptidase. The third member of the oxytocinase subfamily of aminopeptidases. J. Biol. Chem. 278, 32275–32283 (2003).

    Article  CAS  Google Scholar 

  53. Ojcius, D.M., Gapin, L., Kanellopoulos, J.M. & Kourilsky, P. Is antigen processing guided by major histocompatibility complex molecules? FASEB J. 8, 974–978 (1994).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  55. Collins, E.J., Garboczi, D.N. & Wiley, D.C. Three-dimensional structure of a peptide extending from one end of a class I MHC binding site. Nature 371, 626–629 (1994).

    Article  CAS  Google Scholar 

  56. Ojcius, D.M., Langlade-Demoyen, P., Gachelin, G. & Kourilsky, P. Role for MHC class I molecules in selecting and protecting high affinity peptides in the presence of proteases. J. Immunol. 152, 2798–2810 (1994).

    CAS  Google Scholar 

  57. Gil-Torregrosa, B.C., Raul Castano, A. & Del Val, M. Major histocompatibility complex class I viral antigen processing in the secretory pathway defined by the trans-Golgi network protease furin. J. Exp. Med. 188, 1105–1116 (1998).

    Article  CAS  Google Scholar 

  58. Gil-Torregrosa, B.C., Castano, A.R., Lopez, D. & Del Val, M. Generation of MHC class I peptide antigens by protein processing in the secretory route by furin. Traffic 1, 641–651 (2000).

    Article  CAS  Google Scholar 

  59. Thomas, G. Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat. Rev. Mol. Cell Biol. 3, 753–766 (2002).

    Article  CAS  Google Scholar 

  60. Momburg, F., Neefjes, J.J. & Hammerling, G.J. Peptide selection by MHC-encoded TAP transporters. Curr. Opin. Immunol. 6, 32–37 (1994).

    Article  CAS  Google Scholar 

  61. Lopez, D. & Del Val, M. Selective involvement of proteasomes and cysteine proteases in MHC class I antigen presentation. J. Immunol. 159, 5769–5772 (1997).

    CAS  Google Scholar 

  62. Del-Val, M. & Lopez, D. Multiple proteases process viral antigens for presentation by MHC class I molecules to CD8+ T lymphocytes. Mol. Immunol. 39, 235–247 (2002).

    Article  CAS  Google Scholar 

  63. Lopez, D., Gil-Torregrosa, B.C., Bergmann, C. & Del Val, M. Sequential cleavage by metallopeptidases and proteasomes is involved in processing HIV-1 ENV epitope for endogenous MHC class I antigen presentation. J. Immunol. 164, 5070–5077 (2000).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  67. Levy, F. et al. The final N-terminal trimming of a subaminoterminal proline-containing HLA class I-restricted antigenic peptide in the cytosol is mediated by two peptidases. J. Immunol. 169, 4161–4171 (2002).

    Article  CAS  Google Scholar 

  68. Bury, M. et al. Effects of an inhibitor of tripeptidyl peptidase II (Ala-Ala-Phe-chloromethylketone) and its combination with an inhibitor of the chymotrypsin-like activity of the proteasome (PSI) on apoptosis, cell cycle and proteasome activity in U937 cells. Folia Histochem. Cytobiol. 39, 131–132 (2001).

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  70. Kunisawa, J. & Shastri, N. The group II chaperonin TRiC protects proteolytic intermediates from degradation in the MHC class I antigen processing pathway. Mol. Cell 12, 565–576 (2003).

    Article  CAS  Google Scholar 

  71. 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).

    Article  CAS  Google Scholar 

  72. 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).

    Article  CAS  Google Scholar 

  73. Kim, S.I., Pabon, A., Swanson, T.A. & Glucksman, M.J. Regulation of cell-surface major histocompatibility complex class I expression by the endopeptidase EC3.4.24.15 (thimet oligopeptidase). Biochem. J. 375, 111–120 (2003).

    Article  CAS  Google Scholar 

  74. Dunn, A.Y., Melville, M.W. & Frydman, J. Review: cellular substrates of the eukaryotic chaperonin TRiC/CCT. J. Struct. Biol. 135, 176–184 (2001).

    Article  CAS  Google Scholar 

  75. Kandror, O., Sherman, M. & Goldberg, A. Rapid degradation of an abnormal protein in Escherichia coli proceeds through repeated cycles of association with GroEL. J. Biol. Chem. 274, 37743–37749 (1999).

    Article  CAS  Google Scholar 

  76. Samino, Y., Lopez, D., Guil, S., De Leon, P. & Del Val, M. An endogenous HIV envelope-derived peptide without the terminal NH3+ group anchor is physiologically presented by major histocompatibility complex class I molecules. J. Biol. Chem. 279, 1151–1160 (2004).

    Article  CAS  Google Scholar 

  77. Hudrisier, D., Oldstone, M.B. & Gairin, J.E. The signal sequence of lymphocytic choriomeningitis virus contains an immunodominant cytotoxic T cell epitope that is restricted by both H-2Db and H-2Kb molecules. Virology 234, 62–73 (1997).

    Article  CAS  Google Scholar 

  78. Barrett, A.J. et al. Thimet oligopeptidase and oligopeptidase M or neurolysin. Methods Enzymol. 248, 529–556 (1995).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank E. Bishop for assistance in preparation of this manuscript. Supported by grants from the National Institute of General Medical Sciences (A.L.G.) and National Institutes of Health (K.L.R.).

Author information

Authors and Affiliations

  1. Department of Pathology, University of Massachusetts Medical Center, Worcester, 01655, MA, USA

    Kenneth L Rock & Ian A York

  2. Department of Cell Biology, Harvard Medical School, Boston, 02115, Massachusetts, USA

    Alfred L Goldberg

Authors
  1. Kenneth L Rock
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ian A York
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Alfred L Goldberg
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ian A York.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rock, K., York, I. & Goldberg, A. Post-proteasomal antigen processing for major histocompatibility complex class I presentation. Nat Immunol 5, 670–677 (2004). https://doi.org/10.1038/ni1089

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/ni1089

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing