The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage.
Cytotoxic T cells (CTLs) perceive the world through small peptides that are eight to ten amino acids long. These peptides (epitopes) are initially generated by the proteasome, a multi-subunit protease that is responsible for the majority of intra-cellular protein degradation. The proteasome generates the exact C-terminal of CTL epitopes, and the N-terminal with a possible extension. CTL responses may diminish if the epitopes are destroyed by the proteasomes. Therefore, the prediction of the proteasome cleavage sites is important to identify potential immunogenic regions in the proteomes of pathogenic microorganisms (or humans). We have recently shown that NetChop, a neural network-based prediction method, is the best method available at the moment to do such predictions; however, its performance is still lower than desired. Here, we use novel sequence encoding methods and show that the new version of NetChop predicts approximately 10% more of the cleavage sites correctly while lowering the number of false positives with close to 15%. With this more reliable prediction tool, we study two important questions concerning the function of the proteasome. First, we estimate the N-terminal extension of epitopes after proteasomal cleavage and find that the average extension is relatively short. However, more than 30% of the peptides have N-terminal extensions of three amino acids or more, and thus, N-terminal trimming might play an important role in the presentation of a substantial fraction of the epitopes. Second, we show that good TAP ligands have an increased chance of being cleaved by the proteasome, i.e., the specificity of TAP has evolved to fit the specificity of the proteasome. This evolutionary relationship allows for a more efficient antigen presentation.
Nielsen
Morten
M
Center for Biological Sequence Analysis, Technical University of Denmark, BioCentrum-DTU, Building 208, 2800, Lyngby, Denmark. mniel@cbs.dtu.dk
Lundegaard
Claus
C
Lund
Ole
O
Keşmir
Can
C
D000818:Animals; D019295:Computational Biology; D018984:Epitopes, T-Lymphocyte / Q000235:genetics / Q000276:immunology / Q000378:metabolism*; D019143:Evolution, Molecular; D005805:Genes, MHC Class I / Q000276:immunology; D006801:Humans; D008024:Ligands; D046988:Proteasome Endopeptidase Complex / Q000502:physiology*; D016176:T-Lymphocyte Subsets / Q000166:cytology / Q000276:immunology; D013602:T-Lymphocytes, Cytotoxic / Q000166:cytology / Q000276:immunology*
D018984:Epitopes, T-Lymphocyte; D008024:Ligands; D046988:Proteasome Endopeptidase Complex
Immunol Res. 1996;15(4):265-79
8988395
Immunity. 2004 Apr;20(4):495-506
15084277
Immunol Today. 2000 Jul;21(7):317-9
10950502
J Mol Biol. 2000 May 5;298(3):417-29
10772860
Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12504-9
9770515
Science. 1988 Jun 3;240(4857):1285-93
3287615
Immunogenetics. 1999 Nov;50(3-4):213-9
10602881
J Exp Med. 2001 Jul 2;194(1):1-12
11435468
J Mol Biol. 1999 Mar 5;286(4):1251-65
10047495
Int Immunol. 2003 Jul;15(7):781-7
12807816
Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
1438297
Mol Immunol. 2002 Oct;39(3-4):147-64
12200047
Trends Cell Biol. 2001 Jul;11(7):294-7
11413040
Nucleic Acids Res. 2000 Jan 1;28(1):45-8
10592178
Nat Immunol. 2002 Dec;3(12):1177-84
12436110
J Immunol. 2002 Oct 15;169(8):4161-71
12370345
Immunogenetics. 2003 Oct;55(7):437-49
12955356
Nature. 2002 Oct 3;419(6906):480-3
12368856
Bioinformatics. 2004 Jun 12;20(9):1388-97
14962912
J Immunol. 2003 Aug 15;171(4):1741-9
12902473
Immunity. 2003 Jan;18(1):97-108
12530979
Nat Immunol. 2002 Dec;3(12):1169-76
12436109
Protein Eng. 2002 Apr;15(4):287-96
11983929
J Exp Med. 1995 Dec 1;182(6):1865-70
7500032
Mol Biol Evol. 1996 May;13(5):666-73
8676741
Nucleic Acids Res. 1990 Oct 25;18(20):6097-100
2172928
EMBO J. 2001 May 15;20(10):2357-66
11350924
J Immunol. 2004 Jan 15;172(2):1083-91
14707082
Protein Sci. 2003 May;12(5):1007-17
12717023