A novel approach to the analysis of SUMOylation with the independent use of trypsin and elastase digestion followed by database searching utilising consecutive residue addition to lysine

Rapid Communications in Mass Spectrometry

Volumn 27, Issue 1, 2013, Pages 127-134

  Chicooree, Navin ^a,b   Griffiths, John R ^a   Connolly, Yvonne ^a   Tan, Chongteik ^a   Malliri, Angeliki ^a   Eyers, Claire E ^b   Smith, Duncan L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; DATABASE SYSTEMS; ELECTROSPRAY IONIZATION; ENZYMES; INFORMATION RETRIEVAL; LIQUID CHROMATOGRAPHY; MUTAGENESIS; SEARCH ENGINES;

DATABASE SEARCHING; ELASTASE; FUNCTIONAL DIVERSITY; ISOPEPTIDES; LINEAR ION TRAP; ORBITRAP; PROTEIN SAMPLES; SEARCHING STRATEGY; SITE DIRECTED MUTAGENESIS; SUMOYLATION;

MASS SPECTROMETRY;

EID: 84871272921     PISSN: 09514198     EISSN: 10970231     Source Type: Journal    
DOI: 10.1002/rcm.6425     Document Type: Article

References (40)

1. E. S. Wizte, W. M. Old, K. A. Resing, N. G. Ahn,. Mapping protein posttranslational modifications with mass spectrometry. Nat. Methods 2005, 4, 798.
2. H. Li, X. Xing, G. Ding, Q. Li, C. Wang, L. Xie, R. Zeng, L. Yixue,. SysPTM: A systematic resource for proteomic research on posttranslational modifications. Mol. Cell. Proteomics 2009, 8, 1839.
3. S. M. Jeram, T. Srikumar, X. D. Zhang, H. A. Eisenhauer, R. Rogers, P. G. A. Pedrioli, M. Matunis, B. Raught,. An improved SUMmONbased methodology for the identification of ubiquitin and ubiquitinlike protein conjugation sites identifies novel ubquitinlike protein chain linkages. Proteomics 2010, 10, 254.
4. S. Isik, K. Sano, K. Tsutsui, M. Seki, T. Enomoto, H. Saitoh,. The SUMO pathway is required to for selective degradation of DNA topoisomerase IIβ induced by a catalytic inhibitor ICRF193. FEBS Lett. 2003, 546, 374.
5. R.T. Hay,. SUMO: A history of modification. Mol. Cell. 2005, 18, 1.
6. E. Meulmeester, F. Melchior,. Cell biology: SUMO. Nature 2008, 452, 709.
7. M. Boyer;Guittaut, K. Birsoy, C. Potel, G. Elliot, E. Jaffray, J. M. Desterro, R. T. Hay, T. Oelgeschlager,. SUMO1 modification of human transcription factor (TF) IID complex subunits: inhibition of TFIID promoterbinding activity through SUMO1 modification of hsTAF5. J. Biol. Chem. 2005, 11, 9937.
8. R. Li, L. Wang, G. Liao, C. M. Guzzo, M. J Matunis, H. Zhu, S. D. Hayward,. SUMO binding by the EpsteinBarr virus protein kinase BGLF4 is crucial for BGLF4 function. J. Virol. 2012. DOI: 10.1128/JVI.0031412.
9. I. H. Ismail, J. P. Gagné, M. C. Caron, D. McDonald, Z. Xu, J. Y. Masson, G. G. Poirier, M. J. Hendzel,. CBX4mediated SUMO modification regulates BMI1 recruitment at sites of DNA damage. Nucleic Acids Res 2012. DOI: 10.1093/nar/gks222.
10. S. H. Baek,. A novel link between SUMO modification and cancer. Cell Cycle 2006, 5, 1492.
11. A. A. Atwood, R. Jerrell, L. Sealy,. Negative regulation of C/EBPbeta1 by SUMOylation in breast cancer cells. PLoS One 2011, 6, 1.
12. M. H. Stindt, S. Carter, A. M. Vigneron, K. M. Ryan, K. H. Vousden,. MDM2 promotes SUMO2/3 modification of p53 to modulate transcriptional activity. Cell Cycle 2011, 10, 3176.
13. J. Yu, D. Zhang, J. Liu, J. Li, Y. Yu, X. R. Wu, C. Huang,. RhoGDI SUMOylation at K138 increases its binding activity to Rho GTPase and its inhibiting cancer cell motility. J. Biol. Chem. 2012. DOI: 10.1074/jbc.M111. 301523.
14. B. Ding, Y. Sun, J. Huang,. Overexpression of SKI oncoprotein leads to P53 degradation through regulation of MDM2 sumoylation. J. Biol. Chem. 2012. DOI: 10.1074/jbc.M111.337469.
15. P. G. A. Pedrioli, B. Raught, X. D. Zhang, R. Rogers, M. Matunis, R. Abersold,. Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nat. Methods 2006, 3, 533.
16. G. RosasAcosta, K. W. Russel, A. Deyrieux, D. H. Rusell, V. G. Wilson,. A universal stragtegy for proteomic studies of SUMO and other ubiquitinlike modifiers. Mol. Cell. Proteomics 2005, 4, 56.
17. F. Galisson, L. Mahrouche, M. Courcelles, E. Bonneil, S. Meloche, M. K. ChelbiAlix, P. Thibault,. A novel proteomics approach to identify SUMOylated proteins and their modification sites in human cells. Mol. Cell. Proteomics 2011, 10, 1.
18. H. H. Hsiao, E. Meulmeester, B. T. C. Frank, F. Melchoir, H. Urlaub,. 'ChopNSpice' a mass spectrometric approach that allows identification of endogenous small ubiquitinlike modifierconjugated peptides. Mol. Cell. Proteomics 2009, 8, 2664.
19. H. J. Cooper, M. H. Tatham, E. Jaffray, J. K. Heath, T. T. Lam, A. G. Marshall, R. T. Hay,. Fourier transform ion cyclotron resonance mass spectrometry for the analysis of small ubiquitinlike modifier (SUMO) modification: Identification of lysines in RanBP2 and SUMO targeted for modification during the E3 AutoSUMOylation reaction. Anal. Chem. 2005, 77, 6310.
20. M. Treier, D. Bohmann, M. Mlodzik,. JUN cooperates with the ETS domain protein pointed to induce photoreceptor R7 fate in the Drosophila eye. Cell 1995, 83, 753.
21. A. Shevchenko, M. Wilm, O. Vorm, M. Mann,. Mass spectrometric sequencing of proteins silverstained polyacrylamide gels. Anal. Chem. 1996, 68, 850.
22. A. Shevchenko, H. Tomas, J. Havli, J.V Olsen, M. Mann,. Ingel digestion for mass spectrometric characterization of proteins and proteomes. Nat. Protocols 2007, 1, 2856.
23. P. L. Ross, Y. N. Huang, J. N. Marchese, B. Williamson, K. Parker, S. Hattan, N. Khainovski, S. Pillai, S. Dey, S. Daniels, S. Purkayastha, P. Juhasz, S. Martin, M. BartletJones, F. He, A. Jacobson, D. J. Pappin,. Multiplexed protein quantitation in Saccharomyces cerevisiae using aminereactive isobaric tagging reagents. Proteomics 2004, 12, 1154.
24. D. N. Perkins, D. J. C. Pappin, D. M. Creasy, J. S. Cottrell,. Electrophoresis 1999, 20, 3551.
25. J. Peng, D. Schwartz, J. E. Elias, C. C. Thoreen, D. Cheng, G. Marsischky, J. Roelofs, D. Finley, S. P. Gygi,. A proteomics approach to understanding protein ubiquitination. Nat. Biotechnol. 2003, 8, 921.
26. J. Peng, S. P. Gygi,. Proteomics: the move to mixtures. J. Mass Spectrom. 2001, 361, 83.
27. J. L. A. Marotti, R. Newitt, Y. Wang, R. Aebersold, H. G. Dohlman,. Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry 2002, 41, 5067.
28. M. R. E. Warren, C. E. Parker, V. Mocanu, D. Klapper, C. H. Borchers,. Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination. Rapid. Commun. Mass Spectrom. 2005, 19, 429.
29. B. Keil,. Specificity of Proteolysis. SpringerVerlag, Berlin, 1992.
30. J. V. Olsen, S. Ong, M. Mann,. Trypsin cleaves exclusively Cterminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3, 608.
31. J. Rodriguez, N. Gupta, R. D. Smith, P. A. Pevzner,. Does trypsin cut before proline? J. Proteome Res. 2008, 7, 300.
32. J. M. Burkhart, C. Schumbrutzki, S. Wortelkamp, A. Sickmann, R. P. Zahedi,. Systematic and quantitative comparison of digest efficiency and specificity reveals the impact of trypsin quality on MSbased proteomics. J. Proteomics 2011, 4, 1454.
33. P. Picotti, R. Abersold, B. Domon,. The implications of proteolytic background for shotgun proteomics. Mol. Cell. Proteomics 2007, 6, 1589.
34. J. Schimmel, K. M. Larsen, M. Matic, M. V. Hagen, J. Cox, M. Mann, J. S. Andersen, A. C. O. Vertegaal,. The ubiquitinproteasome system is a key component of the SUMO2/3 cycle. Mol. Cell. Proteomics 2008, 7, 2107.
35. N. J. Denis, J. Vasliescu, J. P. Lambert, J. C. Smith, D. Figeys,. Tryptic digestion of ubiquitin standards reveals an improved strategy for identifying ubiquitinated proteins by mass spectrometry. Proteomics 2007, 7, 868.
36. -June 2, 2006.
37. Q. Dumont, D. L. Donaldson, W. P. Griffith,. Screening method for isopeptides from small ubiquitinrelated modifier20. Conjugated proteins by ion mobility mass spectrometry. Anal. Chem. 2011, 83, 9638.
38. M. J. Matunis, E. Coutavas, G. Blobel,. A novel ubiquitinlike modification modulates the partitioning of the RanGTPaseactivating protein RanGAP1 between the cytosol and the nuclear pore complex. J. Cell Biol. 1996, 135, 1457.
39. R. Mahajan, C. Delphin, T. Guan, L. Gerace, F. Melchior,. A small ubiquitinrelated polypeptide involved in targeting RanGAP1 to nuclear pore complex protein RanBP2. Cell 1997, 88, 97.
40. M. Knuesel, H. T. Cheung, M. Hamady, K. K. Barthel, X. A. Liu,. Method of mapping protein sumoylation sites by mass spectrometry using a modified small ubiquitinlike modifier 1 (Sumo1) and a computational program. Mol. Cell. Proteomics 2005, 4, 1626.