The path of no return—Truncated protein N-termini and current ignorance of their genesis

Proteomics

Volumn 15, Issue 14, 2015, Pages 2547-2552

  Fortelny, Nikolaus ^a   Pavlidis, Paul ^a   Overall, Christopher M ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Alternative translation; Protease cleavage; Protease web; Systems biology; TAILS; Terminomics; TopFIND

Indexed keywords

PROTEIN; PROTEINASE; PROTEOME;

ALTERNATIVE RNA SPLICING; AMINO TERMINAL SEQUENCE; ARTICLE; COMPUTER PROGRAM; HUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN DATABASE; PROTEIN PROCESSING;

EID: 85027932761     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201500043     Document Type: Article

References (27)

1. Gaudet, P., Michel, P.-A., Zahn-Zabal, M., Cusin, I. et al., The neXtProt knowledgebase on human proteins: current status. Nucleic Acids Res. 2015, 43, D764–D770.
2. Overall, C. M., Can proteomics fill the gap between genomics and phenotypes? J. Proteomics 2014, 100, 1–2.
3. Lange, P. F., Overall, C. M., Protein TAILS: when termini tell tales of proteolysis and function. Curr. Opin. Chem. Biol. 2013, 17, 73–82.
4. Kleifeld, O., Doucet, A., auf dem Keller, U., Prudova, A. et al., Isotopic labeling of terminal amines in complex samples identifies protein N-termini and protease cleavage products. Nat. Biotechnol. 2010, 28, 281–288.
5. Gevaert, K., Goethals, M., Martens, L., Van Damme, J. et al., Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides. Nat. Biotechnol. 2003, 21, 566–569.
6. auf dem Keller, U., Prudova, A., Eckhard, U., Fingleton, B., Overall, C. M., Systems-level analysis of proteolytic events in increased vascular permeability and complement activation in skin inflammation. Sci. Signal. 2013, 6, rs2.
7. Lange, P. F., Huesgen, P. F., Nguyen, K., Overall, C. M., Annotating N termini for the Human Proteome Project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J. Proteome Res. 2014, 13, 2028–2044.
8. Prudova, A., Serrano, K., Eckhard, U., Fortelny, N. et al., TAILS N-terminomics of human platelets reveals pervasive metalloproteinase dependent proteolytic processing in storage. Blood 2014, 124, e49–e60.
9. Fortelny, N., Yang, S., Pavlidis, P., Lange, P. F., Overall, C. M., Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucleic Acids Res. 2015, 43, D290–D297.
10. Wan, J., Qian, S.-B., TISdb: a database for alternative translation initiation in mammalian cells. Nucleic Acids Res. 2014, 42, D845–850.
11. Flicek, P., Amode, M. R., Barrell, D., Beal, K. et al., Ensembl 2014. Nucleic Acids Res. 2014, 42, D749–D755.
12. Lange, P. F., Overall, C. M., TopFIND, a knowledgebase linking protein termini with function. Nat. Methods 2011, 8, 703–704.
13. Damme, P. V., Gawron, D., Criekinge, W. V., Menschaert, G., N-terminal proteomics and ribosome profiling provide a comprehensive view of the alternative translation initiation landscape in mice and men. Mol. Cell. Proteomics 2014, 13, 1245–1261.
14. Gawron, D., Gevaert, K., Van Damme, P., The proteome under translational control. Proteomics 2014, 14, 2647–2662.
15. Fortelny, N., Cox, J. H., Kappelhoff, R., Starr, A. E., et al., Network analyses reveal pervasive functional regulation between proteases in the Human Protease Web. PLoS Biol. 2014, 12, e1001869.
16. Gillis, J., Ballouz, S., Pavlidis, P., Bias tradeoffs in the creation and analysis of protein–protein interaction networks. J. Proteomics 2014, 100, 44–54.
17. Rawlings, N. D., Barrett, A. J., Bateman, A., MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 2012, 40, D343–D350.
18. Turk, B., Targeting proteases: successes, failures and future prospects. Nat. Rev. Drug Discov. 2006, 5, 785–799.
19. Wildes, D., Wells, J. A., Sampling the N-terminal proteome of human blood. Proc. Natl. Acad. Sci. 2010, 107, 4561–4566.
20. Puente, X. S., Sánchez, L. M., Overall, C. M., López-Otín, C., Human and mouse proteases: a comparative genomic approach. Nat. Rev. Genet. 2003, 4, 544–558.
21. Mason, S. D., Joyce, J. A., Proteolytic networks in cancer. Trends Cell Biol. 2011, 21, 228–237.
22. Bellac, C. L., Dufour, A., Krisinger, M. J., Loonchanta, A., et al., Macrophage matrix metalloproteinase-12 dampens inflammation and neutrophil influx in arthritis. Cell Rep. 2014, 9, 618–632.
23. Krisinger, M. J., Goebeler, V., Lu, Z., Meixner, S. C. et al., Thrombin generates previously unidentified C5 products that support the terminal complement activation pathway. Blood 2012, 120, 1717–1725.
24. Crawford, E. D., Seaman, J. E., Agard, N., Hsu, G. W., et al., The DegraBase: a database of proteolysis in healthy and apoptotic human cells. Mol. Cell. Proteomics MCP 2013, 12, 813–824.
25. Mahrus, S., Trinidad, J. C., Barkan, D. T., Sali, A. et al., Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 2008, 134, 866–876.
26. Van Damme, P., Staes, A., Bronsoms, S., Helsens, K. et al., Complementary positional proteomics for screening substrates of endo- and exoproteases. Nat. Methods 2010, 7, 512–515.
27. Bienvenut, W. V., Sumpton, D., Martinez, A., Lilla, S., et al., Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features. Mol. Cell. Proteomics 2012, 11, M111.015131.