Quantifying the contribution of defective ribosomal products to antigen production: A model-based computational analysis

Journal of Immunology

Volumn 175, Issue 12, 2005, Pages 7957-7964

  Bulik, Sascha ^a   Peters, Bjoern ^b   Holzhütter, Hermann Georg ^a  

^a HUMBOLDT UNIVERSITY   (Germany)

^b LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; CYCLOHEXIMIDE; DEFECTIVE RIBOSOMAL PRODUCT; EPITOPE; GENE PRODUCT; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; SYNTHETIC PEPTIDE; UNCLASSIFIED DRUG;

ANTIGEN BINDING; ANTIGEN PRESENTATION; ANTIGEN PRESENTING CELL; ARTICLE; CELL SURFACE; COMPUTER MODEL; EPITOPE MAPPING; MAJOR HISTOCOMPATIBILITY COMPLEX; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DEGRADATION; PROTEIN SYNTHESIS; PROTEIN SYNTHESIS INHIBITION; QUANTITATIVE ANALYSIS; RIBOSOME;

EID: 29144458032     PISSN: 00221767     EISSN: None     Source Type: Journal    
DOI: 10.4049/jimmunol.175.12.7957     Document Type: Article

References (40)

1. Goldberg, A. L. 2003. Protein degradation and protection against misfolded or damaged proteins. Nature 426: 895-899.
2. Ciechanover, A., and A. L. Schwanz. 2002. Ubiquitin-mediated degradation of cellular proteins in health and disease, Hepatology 35: 3-6.
3. Nussbaum, A. K., T. P. Dick, W. Keilholz, M. Schirle, S. Stevanovic, K. Dietz, W. Heinemeyer, M. Groll, D. H. Wolf, R. Huber, et al. 1998. Cleavage motifs of the yeast 20S proteasome β subunits deduced from digests of enolase 1. Proc. Natl. Acad. Sci. USA 95: 12504-12509.
4. Akopian, T. N., A. F. Kisselev, and A. L. Goldberg. 1997. Processive degradation of proteins and other catalytic properties of the proteasome from Thermoplasma acidophilum. J. Biol. Chem. 272: 1791-1798.
5. Reits, E., J, Neijssen, C. Herberts, W. Benckhuijsen, L. Janssen, J. W. Drijfhout, and J. Neefjes. 2004. A major role for TPPII in trimming proteasomal degradation products for MHC class I antigen presentation. Immunity 20: 495-506.
6. Shastri, N., S. Schwab, and T. Serwold. 2002. Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules. Annu. Rev. Immunol 20: 463-493.
7. Varshavsky, A., G. Turner, F. Du, and Y. Xie. 2000. Felix Hoppe-Seyler Lecture 2000: the ubiquitin system and the N-end rule pathway. Biol. Chem. 381: 779-789.
8. Varshavsky, A. 1996. The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 93: 12142-12149.
9. Grant, E. P., M. T. Michalek, A. L. Goldberg, and K. L. Rock. 1995. Rate of antigen degradation by the ubiquitin-proteasome pathway influences MHC class I presentation. J. Immunol. 155: 3750-3758.
10. Khan, S., R. de Giuli, G. Schmidtke, M. Bruns, M. Buchmeier, M. van den Broek, and M. Groettrup. 2001. Cutting edge: neosynthesis is required for the presentation of a T cell epitope from a long-lived viral protein. J. Immunol. 167: 4801-4804.
11. Yewdell, J. W., L. C. Anton, and J. R. Bennink. 1996. Defective ribosomal products (DRiPs): a major source of antigenic peptides for MHC class I molecules? J. Immunol. 157: 1823-1826.
12. Turner, G. C., and A. Varshavsky. 2000. Detecting and measuring cotranslational protein degradation in vivo. Science 289: 2117-2120.
13. Schild, H., and H. G. Rammensee. 2000, Perfect use of imperfection. Nature 404: 709-710.
14. Reits, E. A., J. C. Vos, M. Gromme, and J. Neefjes. 2000. The major substrates for TAP in vivo are derived from newly synthesized proteins. Nature 404: 774-778.
15. Schubert, U., L. C. Anton, J. Gibbs, C. C. Norbury, J. W. Yewdell, and J. R. Bennink. 2000. Rapid degradation of a large fraction of newly synthesized proteins by proteasomes. Nature 404: 770-774.
16. Princiotta, M. F., D. Finzi, S. B. Qian, J. Gibbs, S. Schuchmann, F. Buttgereit, J. R. Bennink, and J. W. Yewdell. 2003. Quantitating protein synthesis, degradation, and endogenous antigen processing. Immunity 18: 343-354.
17. Kloetzel, P. M. 2004. The proteasome and MHC class I antigen processing. Biochim. Biophys. Acta. 1695: 225-233.
18. Feldman, M., and G. Yagil. 1969. Does cycloheximide interfere with protein degradation? Biochem. Biophys. Res. Commun. 37: 198-203.
19. Goldberg, A. L., and A. C. St John. 1976. Intracellular protein degradation in mammalian and bacterial cells: part 2. Annu. Rev. Biochem. 45: 747-803.
20. Amenta, J. S., M. J. Sargus, and F. M. Baccino. 1978. Inhibition of basal protein degradation in rat embryo fibroblasts by cycloheximide: correlation with activities of lysosomal proteases. J. Cell. Physiol. 97: 267-283.
21. Wildenthal, K., and E. E. Griffin. 1976. Reduction by cycloheximide of lysosomal proteolytic enzyme activity and rate of protein degradation in organ-cultured hearts. Biochim. Biophys. Acta. 444: 519-524.
22. Amshoff, C., H. M. Jack, and I. G. Haas. 1999. Cycloheximide, a new tool to dissect specific steps in ER-associated degradation of different substrates. Biol. Chem. 380: 669-677.
23. Lee, H. K., and L. Marzella. 1994. Regulation of intracellular protein degradation with special reference to lysosomes: role in cell physiology and pathology. Int. Rev. Exp. Pathol. 35: 39-147.
24. Gerlinger, U. M., R. Guckel, M. Hoffmann, D. H. Wolf, and W. Hilt. 1997. Yeast cycloheximide-resistant crl mutants are proteasome mutants defective in protein degradation. Mol. Biol. Cell 8: 2487-2499.
25. Lyakhov, D. L., B. He, X. Zhang, F. W. Studier, J. J. Dunn, and W. T. McAllister. 1998. Pausing and termination by bacteriophage T7 RNA polymerase. J. Mol. Biol. 280: 201-213.
26. Czaplinski. K., M. J. Ruiz-Echevarria, C. I. Gonzalez, and S. W. Peltz. 1999. Should we kill the messenger? The role of the surveillance complex in translation termination and mRNA turnover. BioEssays 21: 685-696,
27. Peters, B., S. Bulik, R. Tampe, P. M. Van Endert, and H. G. Holzhutter. 2003. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J. Immunol. 171: 1741-1749.
28. Reits, E., A. Griekspoor, J. Neijssen, T. Groothuis, K. Jalink, P. van Veelen, H. Janssen, J. Calafat, J. W. Drijfhout, and J. Neefjes. 2003. Peptide diffusion, protection, and degradation in nuclear and cytoplasmic compartments before antigen presentation by MHC class I. Immunity 18: 97-108.
29. Esquivel, F., J. Yewdell, and J. Bennink. 1992. RMA/S cells present endogenously synthesized cytosolic proteins to class I-restricted cytotoxic T lymphocytes. J. Exp. Med. 175: 163-168.
30. Villanueva, M. S., P. Fischer, K. Feen, and E. G. Pamer. 1994. Efficiency of MHC class I antigen processing: a quantitative analysis. Immunity 1: 479-489.
31. Montoya, M., and M. Del Val. 1999. Intracellular rate-limiting steps in MHC class I antigen processing. J. Immunol. 163: 1914-1922.
32. Yewdell, J. W., E. Reits, and J. Neefjes. 2003. Making sense of mass destruction: quantitating MHC class I antigen presentation. Nat. Rev. Immunol. 3: 952-961.
33. Anton, L. C., U. Schubert, I. Bacik, M. F. Princiotta, P. A. Wearsch, J. Gibbs. P. M. Day, C. Realini, M. C. Rechsteiner, J. R. Bennink, and J. W. Yewdell. 1999. Intracellular localization of proteasomal degradation of a viral antigen. J. Cell Biol. 146: 113-124.
34. Cascio, P., C. Hilton, A. F. Kisselev, K. L. Rock, and A. L. Goldberg. 2001. 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide. EMBO J. 20: 2357-2366.
35. York, I. A., A. X. Mo, K. Lemerise, W. Zeng, Y. Shen, C. R. Abraham, T. Saric, A. L. Goldberg, and K. L. Rock. 2003. The cytosolic endopeptidase, thimet oligopeptidase, destroys antigenic peptides and limits the extent of MHC class I antigen presentation. Immunity 18: 429-440.
36. Serwold, T., F. Gonzalez, J. Kim, R. Jacob, and N. Shastri, 2002. ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum. Nature 419: 480-483.
37. York, I. A., S. C. Chang, T. Saric, J. A. Keys, J. M. Favreau, A. L. Goldberg, and K. L. Rock. 2002. The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues. Nat, Immunol. 3: 1177-1184.
38. Poole, B., and M. Wibo. 1973. Protein degradation in cultured cells: the effect of fresh medium, fluoride, and iodoacetate on the digestion of cellular protein of rat fibroblasts. J. Biol. Chem. 248: 6221-6226.
39. May, R. M. 2004. Uses and abuses of mathematics in biology. Science 303: 790-793.
40. Drake, J. W. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl. Acad. Sci. USA 88: 7160-7164.