Profiling constitutive proteolytic events in vivo

Biochemical Journal

Volumn 407, Issue 1, 2007, Pages 41-48

  Timmer, John C ^a,b   Enoksson, Mari ^a   Wildfang, Eric ^a   Zhu, Wenhong ^a   Igarashi, Yoshinobu ^a   Denault, Jean Benard ^a,f   Ma, Yuliang ^a   Dummitt, Benjamin ^c   Chang, Yie Hwa ^c   Mast, Alan E ^d   Eroshkin, Alexey ^a   Smith, Jeffrey W ^a   Tao, W Andy ^e   Salvesen, Guy S ^a,b  

^a BURNHAM INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d BLOOD RESEARCH INSTITUTE   (United States)

^e PURDUE UNIVERSITY   (United States)

^f UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

Mass spectrometry; Methionine aminopeptidase (MetAP); Mitochondrial peptidase; N terminal labelling; Peptidase; Protease; Signal peptidase

Indexed keywords

ESCHERICHIA COLI; GENE ENCODING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PROTEOLYSIS;

METHIONINE AMINOPEPTIDASE (METAP); MITOCHONDRIAL PEPTIDASE; N-TERMINAL LABELING; SIGNAL PEPTIDASE;

ENZYMES;

METHIONYL AMINOPEPTIDASE; PROTEINASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BIOTINYLATION; CONTROLLED STUDY; ESCHERICHIA COLI; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ESCHERICHIA COLI;

AMINO ACID SEQUENCE; AMINOPEPTIDASES; ANIMALS; APROTININ; BLOOD PROTEINS; CASPASES; CELLS, CULTURED; CHROMATOGRAPHY, LIQUID; GENOME, FUNGAL; HUMANS; METHYLUREA COMPOUNDS; MICE; MITOCHONDRIA; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; PEPTIDE HYDROLASES; PEPTIDES; PROTEOME; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 35148891761     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20070775     Document Type: Article

References (37)

1. Rawlings, N. D., Morton, F. R. and Barrett, A. J. (2006) MEROPS: the peptidase database. Nucleic Acids Res. 34, D270-D272
2. Lopez-Otin, C. and Overall, C. M. (2002) Protease degradomics: a new challenge for proteomics. Nat. Rev. Mol. Cell Biol. 3, 509-519
3. Salvesen, G. S. and Dixit, V. M. (1997) Caspases: intracellular signaling by proteolysis. Cell 91, 443-446
4. Overall, C. M. and Dean, R. A. (2006) Degradomics: systems biology of the protease web. Pleiotropic roles of MMPs in cancer. Cancer Metastasis Rev. 25, 69-75
5. Ding, L., Coombs, G. S., Strandberg, L., Navre, M., Corey, D. R. and Madison, E. L. (1995) Origins of the specificity of tissue-type plasminogen activator. Proc. Natl. Acad. Sci. U.S.A. 92, 7627-7631
6. Smith, M., Shi, L. and Navre, M. (1995) Rapid identification of highly active and selective substrates for stromelysin and matrilysin using bacteriophage peptide display libraries. J. Biol. Chem. 270, 6440-6449
7. Thornberry, N. A., Rano, T. A., Peterson, E. P., Rasper, D. M., Timkey, T., Garcia-Calvo, M., Houtzager, V. M., Nordstrom, P. A., Roy, S., Vaillancourt, J. P. et al. (1997) A combinatorial approach defines specificities of members of the caspase family and granzyme B: functional relationships established for key mediators of apoptosis. J. Biol. Chem. 272, 17907-17911
8. Stennicke, H. R., Renatus, M., Meldal, M. and Salvesen, G. S. (2000) Internally quenched fluorescent peptide substrates disclose the subsite preferences of human caspases 1, 3, 6, 7 and 8. Biochem. J. 350, 563-568
9. Deng, S. J., Bickert, D. M., Mitchell, J. L., Lambert, M. H., Blackburn, R. K., Carter, III, H. L., Neugebauer, J., Pahel, G., Weiner, M. P. and Moss, M. L. (2000) Substrate specificity of human collagenase 3 assessed using a phage-displayed peptide library. J. Biol. Chem. 275, 31422-31427
10. Harris, J. L., Backes, B. J., Leonetti, F., Mahrus, S., Ellman, J. A. and Craik, C. S. (2000) Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. Proc. Natl. Acad. Sci. U.S.A. 97, 7754-7759
11. Nazif, T. and Bogyo, M. (2001) Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. Proc. Natl. Acad. Sci. U.S.A. 98, 2967-2972
12. Turk, B. E., Huang, L. L., Piro, E. T. and Cantley, L. C. (2001) Determination of protease cleavage site motifs using mixture-based oriented peptide libraries. Nat. Biotechnol. 19, 661-667
13. α-acetyl transferase families. Trends Biochem. Sci. 23, 263-267
14. Paetzel, M., Karla, A., Strynadka, N. C. and Dalbey, R. E. (2002) Signal peptidases. Chem. Rev. 102, 4549-4580
15. Ito, A. (1999) Mitochondrial processing peptidase: multiple-site recognition of precursor proteins. Biochem. Biophys. Res. Commun. 265, 611-616
16. Zuo, S., Guo, Q., Ling, C. and Chang, Y. H. (1995) Evidence that two zinc fingers in the methionine aminopeptidase from Saccharomyces cerevisiae are important for normal growth. Mol. Gen. Genet. 246, 247-253
17. Ellerby, H. M., Martin, S. J., Ellerby, L. M., Naiem, S. S., Rabizadeh, S., Salvesen, G. S., Casiano, C. A., Cashman, N. R., Green, D. R. and Bredesen, D. E. (1997) Establishment of a cell-free system of neuronal apoptosis: comparison of premitochondrial, mitochondrial, and postmitochondrial phases. J. Neurosci. 17, 6165-6178
18. Kimmel, J. R. (1967) Guanidination of proteins. Methods Enzymol. 11, 584-589
19. Beardsley, R. L., Karty, J. A. and Reilly, J. P. (2000) Enhancing the intensities of lysine-terminated tryptic peptide ions in matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 14, 2147-2153
20. Warwood, S., Mohammed, S., Cristea, I. M., Evans, C., Whetton, A. D. and Gaskell, S. J. (2006) Guanidination chemistry for qualitative and quantitative proteomics. Rapid Commun. Mass Spectrom. 20, 3245-3256
21. Enoksson, M., Li, J., Ivancic, M. M., Timmer, J. C., Wildfang, E., Eroshkin, A., Salvesen, G. S. and Tao, W. A. (2007) Identification of proteolytic cleavage sites by quantitative proteomics. J. Proteome Res. 6, 2850-2858
22. Elias, J. E., Haas, W., Faherty, B. K. and Gygi, S. P. (2005) Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2, 667-675
23. Polevoda, B. and Sherman, F. (2003) N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins. J. Mol. Biol. 325, 595-622
24. Hirel, P. H., Schmitter, M. J., Dessen, P., Fayat, G. and Blanquet, S. (1989) Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. Proc. Natl. Acad. Sci. U.S.A. 86, 8247-8251
25. Frottin, F., Martinez, A., Peynot, P., Mitra, S., Holz, R. C., Giglione, C. and Meinnel, T. (2006) The proteomics of N-terminal methionine cleavage. Mol. Cell. Proteomics 5, 2336-2349
26. Bendtsen, J. D., Nielsen, H., von Heijne, G. and Brunak, S. (2004) Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783-795
27. Gakh, O., Cavadini, P. and Isaya, G. (2002) Mitochondrial processing peptidases. Biochim. Biophys. Acta 1592, 63-77
28. Luo, W., Chen, X., Fang, H. and Green, N. (2003) Factors governing nonoverlapping substrate specificity by mitochondrial inner membrane peptidase. J. Biol. Chem. 278, 4943-4948
29. Nedelkov, D., Kiernan, U. A., Niederkofler, E. E., Tubbs, K. A. and Nelson, R. W. (2005) Investigating diversity in human plasma proteins. Proc. Natl. Acad. Sci. U.S.A. 102, 10852-10857
30. Turner, A. J. (2004) Membrane alanyl aminopeptidase. In Handbook of Proteolytic Enzymes (Barrett, A. J., Rawlings, N. D. and Woessner, J. F., eds.), pp. 289-294, Elsevier, London
31. Kelly, T. (2005) Fibroblast activation protein-α and dipeptidyl peptidase IV (CD26): cell-surface proteases that activate cell signaling and are potential targets for cancer therapy Drug Resist. Updat. 8, 51-58
32. Wiedeman, P. E. and Trevillyan, J. M. (2003) Dipeptidyl peptidase IV inhibitors for the treatment of impaired glucose tolerance and type 2 diabetes. Curr. Opin. Invest. Drugs 4, 412-420
33. Link, A. J., Robison, K. and Church, G. M. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18, 1259-1313
34. Gevaert, K., Goethals, M., Martens, L., Van Damme, J., Staes, A., Thomas, G. R. and Vandekerckhove, J. (2003) Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 21, 566-569
35. McDonald, L., Robertson, D. H., Hurst, J. L. and Beynon, R. J. (2005) Positional proteomics: selective recovery and analysis of N-terminal proteolytic peptides. Nat. Methods 2, 955-957
36. Van den Bergh, G., Clerens, S., Cnops, L., Vandesande, F. and Arckens, L. (2003) Fluorescent two-dimensional difference gel electrophoresis and mass spectrometry identify age-related protein expression differences for the primary visual cortex of kitten and adult cat. J. Neurochem. 85, 193-205
37. Van Damme, P., Martens, L., Van Damme, J., Hugelier, K., Staes, A., Vandekerckhove, J. and Gevaert, K. (2005) Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis. Nat. Methods 2, 771-777