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ER aminopeptidases generate a unique pool of peptides for MHC class I molecules

Nature Immunology volume 2, pages 644–651 (2001)Cite this article

Abstract

We define here the specificity and significance of proteases in the endoplasmic reticulum (ER) that generate peptides for presentation by major histocompatibility complex (MHC) class I molecules. We show that aminopeptidases efficiently trimmed all residues except proline that flank the NH2-termini of antigenic precursors in the ER and caused an accumulation of X-P-Xn peptides. An aminopeptidase inhibitor blocked peptide trimming in the ER and, consequently, the generation of peptide-loaded MHC molecules. Peptide trimming in the ER is therefore a key step in the MHC class I antigen-processing pathway and also explains the paradox of why many MHC class I molecules display peptides with the X-P-Xn motif despite the inability of the transporter associated with antigen processing to transport such peptides from the cytoplasm.

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Figure 1: NH2- or COOH-terminal arginine residue flanking the antigenic peptide is trimmed with differing efficiencies in the ER.
Figure 2: ICP47 blockage of TAP transport and peptide trimming.
Figure 3: The MP-SL8 decapeptide is generated in cells expressing proline-flanked antigenic precursors in the ER.
Figure 4: Leucinethiol differentially inhibits surface expression of peptide–MHC class I complexes.
Figure 5: The presentation of three of nine specific peptides presented by MHC class I molecules was blocked by leucinethiol.
Figure 6: Leucinethiol is a potent and selective inhibitor of aminopeptidase activity in the microsomes.
Figure 7: Leucinethiol inhibits antigen trimming in the ER.
Figure 8: Leucinethiol specifically inhibits aminopeptidase trimming in the ER.

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References

  1. 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).

    Article  CAS  Google Scholar 

  2. Madden, D. R., Gorga, J. C., Strominger, J. L. & Wiley, D. C. The structure of HLA-B27 reveals nonamer self-peptides bound in an extended conformation. Nature 353, 321–325 (1991).

    Article  CAS  Google Scholar 

  3. Pamer, E. G. & Cresswell, P. Mechanisms of MHC class I-restricted antigen processing. Annu. Rev. Immunol. 15, 323–358 (1998).

    Article  Google Scholar 

  4. 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 

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

    Article  CAS  Google Scholar 

  6. Reits, E. A. J., 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).

    Article  CAS  Google Scholar 

  7. 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 

  8. 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 

  9. Attaya, M. et al. Ham-2 corrects the class I antigen-processing defect in RMA-S cells. Nature 355, 647–649 (1992).

    Article  CAS  Google Scholar 

  10. Shepherd, J. C. et al. TAP1-dependent peptide translocation in vitro is ATP dependent and peptide selective. Cell 74, 577–584 (1993).

    Article  CAS  Google Scholar 

  11. Androlowicz, M. J. & Cresswell, P. How selective is the transporter associated with antigen processing? Immunity 5, 1–5 (1996).

    Article  Google Scholar 

  12. Yellen-Shaw, A., Lughlin, C. E., Metrione, R. M. & Eisenlohr, L. C. Murine transporter associated with antigen presentation (TAP) preferences influence class I-restricted T cell responses. J. Exp. Med. 186, 1655–1662 (1997).

    Article  CAS  Google Scholar 

  13. 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 

  14. 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 

  15. Elliott, T., Willis, A., Cerudolo, 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 

  16. Powis, S. J. et al. The Rat cim effect: TAP allele-dependent changes in a class I MHC anchor motif and evidence against C-terminal trimming of peptides in the ER. Immunity 4, 159–165 (1996).

    Article  CAS  Google Scholar 

  17. Snyder, H. L. et al. Two novel routes of transporter associated with antigen processing (TAP)-independent major histocompatibility complex class I antigen processing. J. Exp. Med. 186, 1087–1098 (1997).

    Article  CAS  Google Scholar 

  18. Shastri, N., Serwold, T. & Gonzalez, F. Presentation of endogenous peptide-MHC class I complexes is profoundly influenced by specific C-terminal flanking residues. J. Immunol. 155, 4339–4346 (1995).

    CAS  PubMed  Google Scholar 

  19. Craiu, A., Akopian, T., Goldberg, A. & 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 

  20. Serwold, T. & Shastri, N. Specific proteolytic cleavages limit the diversity of the pool of peptides available to MHC class I molecules in living cells. J. Immunol. 162, 4712–4719 (1999).

    CAS  PubMed  Google Scholar 

  21. 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 

  22. Nielsen, H., Engelbrecht, J., Brunak, S. & von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10, 1–6 (1997).

    Article  CAS  Google Scholar 

  23. Hill, A. et al. Herpes simplex virus turns off the TAP to evade host immunity. Nature 375, 411–415 (1995).

    Article  CAS  Google Scholar 

  24. Yellen-Shaw, A. J., Wherry, E. J., Dubois, G. C. & Eisenlohr, L. C. Point mutation flanking a CTL epitope ablates in vitro and in vivo recognition of a full-length viral protein. J. Immunol. 158, 3227–3234 (1997).

    CAS  PubMed  Google Scholar 

  25. Malarkannan, S., Serwold, T., Nguyen, V., Sherman, L. A. & Shastri, N. The mouse mammary tumor virus env gene is the source of a CD8+ T-cell-stimulating peptide presented by a major histocompatibility complex class I molecule in a murine thymoma. Proc. Natl Acad. Sci. USA 93, 13991–13996 (1996).

    Article  CAS  Google Scholar 

  26. Mentlein, R. Proline residues in the maturation and degradation of peptide hormones and neuropeptides. FEBS Lett. 234, 251–256 (1988).

    Article  CAS  Google Scholar 

  27. Yaron, A. & Naider, F. Proline-dependent structural and biological properties of peptides and proteins. Crit. Rev. Biochem. Mol. Biol. 28, 31–81 (1993).

    Article  CAS  Google Scholar 

  28. Vanhoof, G., Goossens, F., De Meester, I., Hendriks, D. & Scharpe, S. Proline motifs in peptides and their biological processing. FASEB J. 9, 736–744 (1995).

    Article  CAS  Google Scholar 

  29. Malarkannan, S., Goth, S., Buchholz, D. R. & Shastri, N. The role of MHC class I molecules in the generation of endogenous peptide/MHC complexes. J. Immunol. 154, 585–598 (1995).

    CAS  PubMed  Google Scholar 

  30. Rammensee, H. G., Friede, T. & Stevanovic, S. MHC ligands and peptide motifs: First listing. Immunogenetics 41, 178–228 (1995).

    Article  CAS  Google Scholar 

  31. Barber, L. D. et al. Overlap in the repertoires of peptides bound in vivo by a group of related class I HLA-B allotypes. Curr. Biol. 5, 179–190 (1995).

    Article  CAS  Google Scholar 

  32. Van Endert, P. M. et al. The peptide-binding motif for the human transporter associated with antigen processing. J. Exp. Med. 182, 1883–1895 (1995).

    Article  CAS  Google Scholar 

  33. 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  PubMed  Google Scholar 

  34. Storkus, W. J., Zeh, H. J. III, Salter, R. D. & Lotze, M. T. Identification of T-cell epitopes: rapid isolation of class I-presented peptides from viable cells by mild acid elution. J. Immunother. 14, 94–103 (1993).

    Article  CAS  Google Scholar 

  35. Anton, L. C., Yewdell, J. W. & Bennink, J. R. MHC class I-associated peptides produced from endogenous gene products with vastly different efficiencies. J. Immunol. 158, 2535–2542 (1997).

    CAS  PubMed  Google Scholar 

  36. Dick, L. R. et al. Proteolytic processing of ovalbumin and β-galactosidase by the proteasome to yield antigenic peptides. J. Immunol. 152, 3884–3894 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Dick, T. P. et al. Coordinated dual cleavages induced by the proteasome regulator PA28 lead to dominant MHC ligands. Cell 86, 253–262 (1996).

    Article  CAS  Google Scholar 

  38. Niedermann, G. et al. Contribution of proteasome-mediated proteolysis to the hierarchy of epitopes presented by major histocompatibility complex class I molecules. Immunity 2, 289–299 (1995).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  40. Zuberi, A., Christianson, G. J., Mendoza, L. M., Shastri, N. & Roopenian, D. C. Positional cloning and molecular characterization of an immunodominant cytotoxic determinant of the mouse H3 minor histocompatibility complex. Immunity 9, 687–698 (1998).

    Article  CAS  Google Scholar 

  41. Falk, K., Rotzschke, O., Stevanovic, S., Jung, G. & Rammensee, H. G. Pool sequencing of natural HLA-DR, DQ, and DP ligands reveals detailed peptide motifs, constraints of processing, and general rules. Immunogenetics 39, 230–242 (1994).

    Article  CAS  Google Scholar 

  42. Nelson, C. A., Vidavsky, I., Viner, N. J., Gross, M. L. & Unanue, E. R. Amino-terminal trimming of peptides for presentation on major histocompatibility complex class II molecules. Proc. Natl Acad. Sci. USA 94, 628–633 (1997).

    Article  CAS  Google Scholar 

  43. Karttunen, J., Sanderson, S. & Shastri, N. Detection of rare antigen presenting cells by the lacZ T-cell activation assay suggests an expression cloning strategy for T-cell antigens. Proc. Natl Acad. Sci. USA 89, 6020–6024 (1992).

    Article  CAS  Google Scholar 

  44. Malarkannan, S., Afkarian, M. & Shastri, N. A rare cryptic translation product is presented by Kb major histocompatibility complex class I molecule to alloreactive T cells. J. Exp. Med. 182, 1739–1750 (1995).

    Article  CAS  Google Scholar 

  45. Mendoza, L., Villaflor, G., Eden, P., Roopenian, D. C. & Shastri, N. Distinguishing self from nonself. Immunogenicity of the murine H47 locus is determined by a single amino acid substitution in an unusual peptide. J. Immunol. 166, 4438–4445 (2001).

    Article  CAS  Google Scholar 

  46. Mendoza, L. et al. Minors held by majors. The H13 minor histocompatibility locus defined as a peptide/MHC class I complex. Immunity 7, 461–472 (1997).

    Article  CAS  Google Scholar 

  47. Shastri, N., Nguyen, V. & Gonzalez, F. Major histocompatibility class I molecules can present cryptic translation products to T-cells. J. Biol. Chem. 270, 1088–1091 (1995).

    Article  CAS  Google Scholar 

  48. Sanderson, S. & Shastri, N. LacZ inducible peptide/MHC specific T-hybrids. Int. Immunol. 6, 369–376 (1994).

    Article  CAS  Google Scholar 

  49. Shastri, N. & Gonzalez, F. Endogenous generation and presentation of the OVA peptide/Kb complex to T-cells. J. Immunol. 150, 2724–2736 (1993).

    CAS  PubMed  Google Scholar 

  50. Walter, P. & Blobel, G. Preparation of microsomal membranes for cotranslational protein translocation. Meth. Enzymol. 96, 84–93 (1983).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank L. Mendoza and other investigators who provided us with key reagents and S. Schwab for comments on the manuscript. Supported by grants from the NIH (to N. S.).

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  1. Division of Immunology, Department of Molecular and Cell Biology, University of California, Berkeley, 94720-3200, CA, USA

    Thomas Serwold, Stephanie Gaw & Nilabh Shastri

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Correspondence to Nilabh Shastri.

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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). https://doi.org/10.1038/89800

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