Protease degradomics: Mass spectrometry discovery of protease substrates and the CLIP-CHIP, a dedicated DNA microarray of all human proteases and inhibitors

Biological Chemistry

Volumn 385, Issue 6, 2004, Pages 493-504

  Overall, Christopher M ^a   Tam, Eric M ^a   Kappelhoff, Reinhild ^a   Connor, Andrea ^a   Ewart, Tom ^b   Morrison, Charlotte J ^a   Puente, Xose ^c   López Otín, Carlos ^c   Seth, Arun ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b SUNNYBROOK RESEARCH INSTITUTE   (Canada)

^c UNIVERSITY OF OVIEDO   (Spain)

Author keywords

Metalloproteinase; MT1 MMP; Oligonucleotide chip; Proteinase; Proteomics; Transcriptome

Indexed keywords

CARBOXYPEPTIDASE A; COMPLEMENTARY DNA; DNA; INTERLEUKIN 8; MATRIX METALLOPROTEINASE; OLIGONUCLEOTIDE; ONCOPROTEIN; PROTEINASE; PROTEINASE INHIBITOR; TRYPTASE; TUMOR NECROSIS FACTOR ALPHA; TUMOR NECROSIS FACTOR ALPHA CONVERTING ENZYME; WNT PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BREAST CARCINOMA; CARCINOMA CELL; CELL CULTURE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DNA LIBRARY; DNA MICROARRAY; ENZYME ACTIVE SITE; FEMALE; FIBROBLAST; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VIVO STUDY; MASS SPECTROMETRY; PAGET NIPPLE DISEASE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; QUANTITATIVE ANALYSIS; SEQUENCE HOMOLOGY; TANDEM MASS SPECTROMETRY; TISSUE DISTRIBUTION; TWO HYBRID SYSTEM;

BREAST NEOPLASMS; CATALYSIS; CELL LINE; CELL LINE, TUMOR; FEMALE; HUMANS; MAMMARY GLANDS, HUMAN; MASS SPECTROMETRY; MATRIX METALLOPROTEINASES; MATRIX METALLOPROTEINASES, SECRETED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEPTIDE HYDROLASES; PROTEASE INHIBITORS; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; STAINING AND LABELING; SUBSTRATE SPECIFICITY; TWO-HYBRID SYSTEM TECHNIQUES;

EID: 3242777139     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/BC.2004.058     Document Type: Article

References (45)

1. Ball, D.K., Surveyor, G.A., Diehl, J.R., Steffen, C.L., Uzumcu, M., Mirando, M.A. and Brigstock, D.R. (1998). Characterization of 16- to 20-kilodalton (kDa) connective tissue growth factors (CTGFs) and demonstration of proteolytic activity for 38-kDa CTGF in pig uterine luminal flushings. Biol. Reprod. 59, 828-835.
2. Belkin, A.M., Akimov, S.S., Zaritskaya, L.S., Ratnikov, B.I., Deryugina, E.I. and Strongin, A.Y. (2001). Matrix-dependent proteolysis of surface transglutaminase by membrane-type metalloproteinase regulates cancer cell adhesion and locomotion. J. Biol. Chem. 276, 18415-18422.
3. Belperio, J.A., Keane, M.P., Arenberg, D.A., Addison, C.L., Ehlert, J.E., Burdick, M.D. and Strieter, R.M. (2000). CXC chemokines in angiogenesis. J. Leukoc. Biol. 68, 1-8.
4. Billinghurst, R.C., Ionescu, M., Reiner, A., Bourne, R., Rorabeck, C., Mitchell P, Diekmann O, Tschesche, H., Chen, J., Van Wart, H. and Poole, A.R. (1997). Enhanced cleavage of type II collagen by collagenases in osteoarthritic articular cartilage. J. Clin. Invest. 99, 1534-1545.
5. Black, R.A., Rauch, C.T., Kozlosky, C.J., Peschon, J.J., Slack, J.L., Wolfson, M.F., Castner, B.J., Stocking, K.L., Reddy, P., Srinivasan, S. et al. (1997). A metalloproteinase disintegrin that releases tumour-necrosis factor-alpha from cells. Nature 385, 729-733.
6. Brigstock, D.R. (1999). The connective tissue growth factor/cysteine-rich 61/nephroblastoma overexpressed (CCN) family. Endocr. Rev. 20, 189-206.
7. Brigstock, D.R. (2003). The CCN family: a new stimulus package. J. Endocrinol. 178, 169-175.
8. Clark-Lewis, I., Vo, L., Owen, P. and Anderson, J. (1997). Chemical synthesis, purification, and folding of C-X-C and C-C chemokines. Methods Enzymol. 287, 233-250.
9. Deng, S.J., Bickett, D.M., Mitchell, J.L., Lambert, M.H., Blackburn, R.K., Carter, H.L., 3rd, 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. Egeblad, M. and Werb, Z. (2002). New functions for the matrix metalloproteinases in cancer progression. Nat. Rev. Cancer 2, 161-174.
11. Greenbaum, D., Baruch, A., Hayrapetian, L., Darula, Z., Burlingame, A., Medzihradszky, K.F. and Bogyo, M. (2002). Chemical approaches for functionally probing the proteome. Mol. Cell Proteomics 1, 60-68.
12. Grutter, M.G., Fendrich, G., Huber, R. and Bode, W. (1988). The 2.5 Å X-ray crystal structure of the acid-stable proteinase inhibitor from human mucous secretions analysed in its complex with bovine alpha-chymotrypsin. EMBO J. 7, 345-351.
13. Guo, L., Eisenman, J.R., Mahimkar, R.M., Peschon, J.J., Paxton, R.J., Black, R.A. and Johnson, R.S. (2002). A proteomic approach for the identification of cell-surface proteins shed by metalloproteases. Mol. Cell Proteomics 1, 30-36.
14. Gygi, S.P., Corthals, G.L., Zhang, Y., Rochon, Y. and Aebersold, R. (2000). Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97, 9390-9395.
15. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H. and Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999.
16. Haro, H., Crawford, H.C., Fingleton, B., Shinomiya, K., Spengler, D.M. and Matrisian, L.M. (2000). Matrix metalloproteinase 1-dependent release of tumor necrosis factor-alpha in a model of hermiated disc resorption. J. Clin. Invest. 105, 143-150.
17. Hashimoto, G., Inoki, I., Fujii, Y., Aoki, T., Ikeda, E. and Okada, Y. (2002). Matrix metalloproteinases cleave connective tissue growth factor and reactivate angiogenic activity of vascular endothelial growth factor 165. J. Biol. Chem. 277, 36288-36295.
18. Henry, M.T., McMahon, K., Costello, C., Fitzgerald, M.X. and O'Connor, C.M. (2002). Secretory leukocyte proteinase inhibitor and elafin are resistant to degradation by MMP-8. Exp. Lung Res. 28, 85-97.
19. Holmbeck, K., Bianco, P., Caterina, J., Yamada, S., Kromer, M., Kuznetsov, S.A., Mankani, M., Robey, P.G., Poole, A.R., Pidoux, I. et al. (1999). MT1-MMP-deficient mice develop dwarfism, osteopenia, arthritis, and connective tissue disease due to inadequate collagen turnover. Cell 99, 81-92.
20. Hughes, C.E., Caterson, B., Fosang, A.J., Roughley, P.J. and Mort, J.S. (1995). Monoclonal antibodies that specifically recognize neoepitope sequences generated by 'aggrecanase' and matrix metalloproteinase cleavage of aggrecan: application to catabolism in situ and in vitro. Biochem. J. 305, 799-804.
21. Lemons, M.L., Sandy, J.D., Anderson, D.K. and Howland, D.R. (2001). Intact aggrecan and fragments generated by both aggrecanse and metalloproteinase-like activities are present in the developing and adult rat spinal cord and their relative abundance is altered by injury. J. Neurosci. 21, 4772-4781.
22. Liu, Y., Patricelli, M.P. and Cravatt, B.F. (1999). Activity-based protein profiling: the serine hydrolases. Proc. Natl. Acad. Sci. USA 96, 14694-14699.
23. Lopez-Otin, C. and Overall, C.M. (2002). Protease degradomics: a new challenge for proteomics. Nat. Rev. Mol. Cell Biol. 3, 509-519.
24. McQuibban, G.A., Butler, G.S., Gong, J.H., Bendall, L., Power, C., Clark-Lewis, I. and Overall, C.M. (2001). Matrix metalloproteinase activity inactivates the CXC chemokine stromal cell-derived factor-1. J. Biol. Chem. 276, 43503-43508.
25. McQuibban, G.A., Gong, J.H., Tam, E.M., McCulloch, C.A., Clark-Lewis, I. and Overall, C.M. (2000). Inflammation dampened by gelatinase A cleavage of monocyte chemoattractant protein-3. Science 289, 1202-1206.
26. McQuibban, G.A., Gong, J.H., Wong, J.P., Wallace, J.L., Clark-Lewis, I. and Overall, C.M. (2002). Matrix metalloproteinase processing of monocyte chemoattractant proteins generates CC chemokine receptor antagonists with anti-inflammatory properties in vivo. Blood 100, 1160-1167.
27. Morrison, C.J., Butler, G.S., Bigg, H.F., Roberts, C.R., Soloway, P.D. and Overall, C.M. (2001). Cellular activation of MMP-2 (gelatinase A) by MT2-MMP occurs via a TIMP-2-independent pathway. J. Biol. Chem. 276, 47402-47410.
28. Moss, M.L., Jin, S.L., Milla, M.E., Bickett, D.M., Burkhart, W., Carter, H.L., Chen, W.J., Clay, W.C., Didsbury, J.R., Hassler, D. et al. (1997). Cloning of a disintegrin metalloproteinase that processes precursor tumour-necrosis factor-a. Nature 385, 733-736.
29. Nazif, T. and Bogyo, M. (2001). Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. Proc. Natl. Acad. Sci. USA 98, 2967-2972.
30. Ohuchi, E., Imai, K., Fujii, Y., Sato, H., Seiki, M. and Okada, Y. (1997). Membrane type 1 matrix metalloproteinase digests interstitial collagens and other extracellular matrix macromolecules. J. Biol. Chem. 272, 2446-2451.
31. Overall, C.M. (2001). Matrix metalloproteinase substrate binding domains, modules and exosites. Overview and experimental strategies. Methods Mol. Biol. 151, 79-120.
32. Overall, C.M., McQuibban, G.A. and Clark-Lewis, I. (2002). Discovery, of chemokine substrates for matrix metalloproteinases by exosite scanning: a new tool for degradomics. Biol. Chem. 383, 1059-1066.
33. Overall, C.M., Wiebkin, O.W. and Thonard, J.C. (1987). Demonstration of tissue collagenase activity in vivo and its relationship to inflammation severity in human gingiva. J. Periodont. Res. 22, 81-88.
34. Pan, G., Bauer, J.H., Haridas, V., Wang, S., Liu, D., Yu, G., Vincenz, C., Aggarwal, B.B., Ni, J. and Dixit, V.M. (1998). Identification and functional characterization of DR6, a novel death domain-containing TNF receptor. FEBS Lett. 431, 351-356.
35. Pennica, D., Swanson, T.A., Welsh, J.W., Roy, M.A., Lawrence, D.A., Lee, J., Brush, J., Taneyhill, L.A., Deuel, B., Lew, M. et al. (1998). WISP genes are members of the connective tissue growth factor family that are up-regulated in wnt-1-transformed cells and aberrantly expressed in human colon tumors. Proc. Natl. Acad. Sci. USA 95, 14717-14722.
36. Puente, X.S., Sanchez, L.M., Overall, C.M. and Lopez-Otin, C. (2003). Human and mouse proteases: a comparative genomic approach. Nat. Rev. Genet. 4, 544-558.
37. Sato, H., Takino, T., Okada, Y., Cao, J., Shinagawa, A., Yamamoto, E. and Seiki, M. (1994). A matrix metalloproteinase expressed on the surface of invasive tumour cells. Nature 370, 61-65.
38. Seiki, M. (2003). Membrane-type 1 matrix metalloproteinase: a key enzyme for tumor invasion. Cancer Lett. 194, 1-11.
39. Shen, M., Guo, L., Wallace, A., Fitzner, J., Eisenman, J., Jacobson, E. and Johnson, R.S. (2003). Isolation and isotope labeling of cysteine- and methionine-containing tryptic peptides: application to the study of cell surface proteolysis. Mol. Cell Proteomics 2, 315-324.
40. Tam, E.M., Morrison, C.J., Wu, Y.I., Stack, M.S. and Overall, C.M. (2004). Membrane protease functional proteomics: isotope coded affinity tag/tandem mass spectrometry identification of novel MT1-MMP substrates. Proc. Natl. Acad. Sci. USA 101, 6917-6922.
41. Tam, E.M., Wu, Y.I., Butler, G.S., Stack, M.S. and Overall, C.M. (2002). Collagen binding properties of the membrane type-1 matrix metalloproteinase (MT1-MMP) hemopexin C domain. The ectodomain of the 44-kDa autocatalytic product of MT1-MMP inhibits cell invasion by disrupting native type I collagen cleavage. J. Biol. Chem. 277, 39005-39014.
42. 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.
43. Van Damme, J., Decock, B., Conings, R., Lenaerts, J.P., Opdenakker, G. and Billiau, A. (1989). The chemotactic activity for granulocytes produced by virally infected fibroblasts is identical to monocyte-derived interleukin 8. Eur. J. Immunol. 19, 1189-1194.
44. Van den Steen, P.E., Proost, P., Wuyts, A., Van Damme, J. and Opdenakker, G. (2000). Neutrophil gelatinase B potentiates interleukin-8 tenfold by aminoterminal processing, whereas it degrades CTAP-III, PF-4, and GRO-alpha and leaves RANTES and MCP-2 intact. Blood 96, 2673-2681.
45. Yamanaka, H., Makino, K., Takizawa, M., Nakamura, H., Fujimoto, N., Moriya, H., Nemori, R., Sato, H., Seiki, M. and Okada, Y. (2000). Expression and tissue localization of membrane-types 1, 2, and 3 matrix metalloproteinases in rheumatoid synovium. Lab. Invest. 80, 677-687.