Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance

Article metrics


Although cytotoxic T lymphocytes (CTLs) in people infected with human immunodeficiency virus type 1 can potentially target multiple virus epitopes, the same few are recognized repeatedly. We show here that CTL immunodominance in regions of the human immunodeficiency virus type 1 group-associated antigen proteins p17 and p24 correlated with epitope abundance, which was strongly influenced by proteasomal digestion profiles, affinity for the transporter protein TAP, and trimming mediated by the endoplasmatic reticulum aminopeptidase ERAAP, and was moderately influenced by HLA affinity. Structural and functional analyses demonstrated that proteasomal cleavage 'preferences' modulated the number and length of epitope-containing peptides, thereby affecting the response avidity and clonality of T cells. Cleavage patterns were affected by both flanking and intraepitope CTL-escape mutations. Our analyses show that antigen processing shapes CTL response hierarchies and that viral evolution modifies cleavage patterns and suggest strategies for in vitro vaccine optimization.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: SLYNTVATL evolution and HIV p17 epitopes.
Figure 2: Proteasomal digestion of p17.
Figure 3: Antigen processing and presentation of p17.
Figure 4: CTL recognition of SLYNTVATL sequence and length variants.
Figure 5: Structure of HLA-A*0201–SLFNTVATLY and comparison with previously determined 9–amino acid SLYNTVATL variant structures.
Figure 6: Antigen processing of p24.
Figure 7: Cell line–recognition patterns of KK10 peptide forms.

Accession codes


Protein Data Bank


  1. 1

    Yewdell, J.W. Confronting complexity: real-world immunodominance in antiviral CD8+ T cell responses. Immunity 25, 533–543 (2006).

  2. 2

    Altfeld, M. et al. HLA alleles associated with delayed progression to AIDS contribute strongly to the initial CD8+ T cell response against HIV-1. PLoS Med. 3, e403 (2006).

  3. 3

    Bihl, F. et al. Impact of HLA-B alleles, epitope binding affinity, functional avidity, and viral coinfection on the immunodominance of virus-specific CTL responses. J. Immunol. 176, 4094–4101 (2006).

  4. 4

    Goulder, P.J. et al. Substantial differences in specificity of HIV-specific cytotoxic T cells in acute and chronic HIV infection. J. Exp. Med. 193, 181–194 (2001).

  5. 5

    Chen, W., Anton, L.C., Bennink, J.R. & Yewdell, J.W. Dissecting the multifactorial causes of immunodominance in class I-restricted T cell responses to viruses. Immunity 12, 83–93 (2000).

  6. 6

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

  7. 7

    Tenzer, S. et al. Quantitative analysis of prion-protein degradation by constitutive and immuno-20S proteasomes indicates differences correlated with disease susceptibility. J. Immunol. 172, 1083–1091 (2004).

  8. 8

    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).

  9. 9

    Van den Eynde, B.J. & Morel, S. Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome. Curr. Opin. Immunol. 13, 147–153 (2001).

  10. 10

    HIV Molecular Immunology 2006/2007 (eds. Korber, B.T.M. et al.) 53–248 (Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, 2006–2007).

  11. 11

    Iversen, A.K. et al. Conflicting selective forces affect T cell receptor contacts in an immunodominant human immunodeficiency virus epitope. Nat. Immunol. 7, 179–189 (2006).

  12. 12

    Goulder, P.J. & Watkins, D.I. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat. Rev. Immunol. 8, 619–630 (2008).

  13. 13

    Kaslow, R.A. et al. Influence of combinations of human major histocompatibility complex genes on the course of HIV-1 infection. Nat. Med. 2, 405–411 (1996).

  14. 14

    Goulder, P.J. et al. Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS. Nat. Med. 3, 212–217 (1997).

  15. 15

    Schneidewind, A. et al. Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. J. Virol. 82, 5594–5605 (2008).

  16. 16

    Schneidewind, A. et al. Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J. Virol. 81, 12382–12393 (2007).

  17. 17

    Draenert, R. et al. Immune selection for altered antigen processing leads to cytotoxic T lymphocyte escape in chronic HIV-1 infection. J. Exp. Med. 199, 905–915 (2004).

  18. 18

    Milicic, A. et al. CD8+ T cell epitope-flanking mutations disrupt proteasomal processing of HIV-1 Nef. J. Immunol. 175, 4618–4626 (2005).

  19. 19

    Zimbwa, P. et al. Precise identification of a human immunodeficiency virus type 1 antigen processing mutant. J. Virol. 81, 2031–2038 (2007).

  20. 20

    Le Gall, S., Stamegna, P. & Walker, B.D. Portable flanking sequences modulate CTL epitope processing. J. Clin. Invest. 117, 3563–3575 (2007).

  21. 21

    Leslie, A. et al. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J. Exp. Med. 201, 891–902 (2005).

  22. 22

    Ossendorp, F. et al. A single residue exchange within a viral CTL epitope alters proteasome-mediated degradation resulting in lack of antigen presentation. Immunity 5, 115–124 (1996).

  23. 23

    Shimbara, N. et al. Contribution of proline residue for efficient production of MHC class I ligands by proteasomes. J. Biol. Chem. 273, 23062–23071 (1998).

  24. 24

    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).

  25. 25

    Gubler, B. et al. Substrate selection by transporters associated with antigen processing occurs during peptide binding to TAP. Mol. Immunol. 35, 427–433 (1998).

  26. 26

    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).

  27. 27

    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).

  28. 28

    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).

  29. 29

    Altfeld, M. et al. Cellular immune responses and viral diversity in individuals treated during acute and early HIV-1 infection. J. Exp. Med. 193, 169–180 (2001).

  30. 30

    Lee, J.K. et al. T cell cross-reactivity and conformational changes during TCR engagement. J. Exp. Med. 200, 1455–1466 (2004).

  31. 31

    Martinez-Hackert, E. et al. Structural basis for degenerate recognition of natural HIV peptide variants by cytotoxic lymphocytes. J. Biol. Chem. 281, 20205–20212 (2006).

  32. 32

    Streeck, H. et al. Recognition of a defined region within p24 gag by CD8+ T cells during primary human immunodeficiency virus type 1 infection in individuals expressing protective HLA class I alleles. J. Virol. 81, 7725–7731 (2007).

  33. 33

    Bouillot, M. et al. Physical association between MHC class I molecules and immunogenic peptides. Nature 339, 473–475 (1989).

  34. 34

    Huet, S. et al. Structural homologies between two HLA B27-restricted peptides suggest residues important for interaction with HLA B27. Int. Immunol. 2, 311–316 (1990).

  35. 35

    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).

  36. 36

    Nixon, D.F. et al. HIV-1 Gag-specific cytotoxic T lymphocytes defined with recombinant vaccinia virus and synthetic peptides. Nature 336, 484–487 (1988).

  37. 37

    Urban, R.G. et al. A subset of HLA-B27 molecules contains peptides much longer than nonamers. Proc. Natl. Acad. Sci. USA 91, 1534–1538 (1994).

  38. 38

    Betts, M.R. et al. Putative immunodominant human immunodeficiency virus-specific CD8+ T-cell responses cannot be predicted by major histocompatibility complex class I haplotype. J. Virol. 74, 9144–9151 (2000).

  39. 39

    Altfeld, M.A. et al. Identification of dominant optimal HLA-B60- and HLA-B61-restricted cytotoxic T-lymphocyte (CTL) epitopes: rapid characterization of CTL responses by enzyme-linked immunospot assay. J. Virol. 74, 8541–8549 (2000).

  40. 40

    Streeck, H. et al. Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells. PLoS Med. 5, e100 (2008).

  41. 41

    Almeida, J.R. et al. Superior control of HIV-1 replication by CD8+ T cells is reflected by their avidity, polyfunctionality, and clonal turnover. J. Exp. Med. 204, 2473–2485 (2007).

  42. 42

    Wearsch, P.A. & Cresswell, P. Selective loading of high-affinity peptides onto major histocompatibility complex class I molecules by the tapasin-ERp57 heterodimer. Nat. Immunol. 8, 873–881 (2007).

  43. 43

    Brumme, Z.L. et al. Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1. PLoS Pathog. 3, e94 (2007).

  44. 44

    Goulder, P.J. & Watkins, D.I. HIV and SIV CTL escape: implications for vaccine design. Nat. Rev. Immunol. 4, 630–640 (2004).

  45. 45

    Goulder, P.J. et al. Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 412, 334–338 (2001).

  46. 46

    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).

  47. 47

    Wilson, J.D. et al. Oligoclonal expansions of CD8+ T cells in chronic HIV infection are antigen specific. J. Exp. Med. 188, 785–790 (1998).

  48. 48

    Gao, X. et al. AIDS restriction HLA allotypes target distinct intervals of HIV-1 pathogenesis. Nat. Med. 11, 1290–1292 (2005).

  49. 49

    Burgevin, A. et al. A detailed analysis of the murine TAP transporter substrate specificity. PLoS ONE 3, e2402 (2008).

  50. 50

    Sylvester-Hvid, C. et al. Establishment of a quantitative ELISA capable of determining peptide-MHC class I interaction. Tissue Antigens 59, 251–258 (2002).

Download references


We thank the patients for donating samples; B. Baadegaard and L.P. Jensen for patient management; D. Hass, T. Rostron, J. Frankland and J. Forsch for technical assistance; and N. Willcox for discussions. Supported by the Novo Nordisk Foundation, the Danish AIDS foundation, the Deutsche Forschungsgemeinschaft (Sonderforschungsbereich 490, E6, Z3), the Genomes2Vaccines Specific Targeted Research Project, Sixth Framework Programme (LSHB-CT-2003-503231), the Hochschulbauförderungsgesetz Program (HBFG-122-605), the Forschungszentrum Immunologie at the University of Mainz, the Nuffield Dominions Trust, Cancer Research UK, the European Union (LSHG-CT-2006-031220, LSHC-CT-2006-518234 and HEALTH-2007-222773), the Wellcome Trust, The James Martin 21st Century School at the University of Oxford, the National Institute for Health Research Biomedical Research Centre Programme, and the UK Medical Research Council.

Author information

A.K.N.I. conceived and designed the overall study and wrote the manuscript; S.T., H.S., S.B., P.v.E. and A.K.N.I. planned and supervised experiments; S.T., E.W., A.B., G.S.-J., L.F., K.L., C.-h.C., M.H., M.W., N.A. and A.K.N.I. did experiments; S.T., H.S., S.B., G.S.-J., E.Y.J., P.K., P.v.E. and A.K.N.I. analyzed data; J.G. and A.K.N.I. provided patient samples; S.B., P.v.E., A.J.M., L.F., A.K.N.I. and H.S. provided reagents; and S.T., S.B., H.S., P.K., L.F., G.S.-J., E.Y.J. and P.v.E. contributed intellectual input.

Correspondence to Astrid K N Iversen.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 1–3 (PDF 5449 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tenzer, S., Wee, E., Burgevin, A. et al. Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance. Nat Immunol 10, 636–646 (2009) doi:10.1038/ni.1728

Download citation

Further reading