Evaluation of D10-Leu metabolic labeling coupled with MALDI-MS analysis in studying the response of the yeast proteome to H2O 2 challenge

Journal of Proteome Research

Volumn 5, Issue 10, 2006, Pages 2539-2546

  Jiang, Heng ^a   English, Ann M ^a  

^a Gina Cody School of Engineering and Computer Science   (Canada)

Author keywords

2DE; D10 Leu; H 2O2; MALDI TOF MS; Metabolic labeling; S. cerevisiae; SRIH2O2

Indexed keywords

HYDROGEN PEROXIDE; LEUCINE; PROTEOME; DEUTERIUM; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CHEMICAL LABELING; CONTROLLED STUDY; FUNGUS GROWTH; GLYCOLYSIS; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; OXIDATIVE STRESS; PRIORITY JOURNAL; PROTEIN CONTENT; PROTEOMICS; QUANTITATIVE ANALYSIS; SACCHAROMYCES CEREVISIAE; TWO DIMENSIONAL ELECTROPHORESIS; CHEMISTRY; DRUG EFFECT; ENZYMOLOGY; EVALUATION; MASS SPECTROMETRY; METABOLISM; METHODOLOGY;

DEUTERIUM; GLYCOLYSIS; HYDROGEN PEROXIDE; LEUCINE; OXIDATIVE STRESS; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33750140392     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr060019m     Document Type: Article

References (51)

1. Goshe, M. B.; Smith, R. D. Stable isotope-coded proteomic mass spectrometry. Curr. Opin. Biotechnol. 2003, 14 (1), 101-109.
2. Beynon, R. J.; Pratt, J. M. Metabolic labeling of proteins for proteomics. Mol. Cell Proteomics 2005, 4 (7), 857-872.
3. Jiang, H.; English, A. M. Quantitative analysis of the yeast proteome by incorporation of isotopically labeled leucine. J. Proteome Res. 2002, 1 (4), 345-350.
4. Trabalzini, L.; Paffetti, A.; Scaloni, A.; Talamo, P.; Ferro, E.; Coratza, G.; Bovalini, L.; Lusini, P.; Martelli, P.; Santucci, A. Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae. Biochem. J. 2003, 370 (Pt 1), 35-46.
5. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
6. Hu, Y.; Wang, G.; Chen, G. Y.; Fu, X.; Yao, S. Q. Proteome analysis of Saccharomyces cerevisiae under metal stress by two-dimensional differential gel electrophoresis. Electrophoresis 2003, 24 (9), 1458-1470.
7. 2 stimulon in Saccharomyces cerevisiae. J. Biol Chem. 1998, 273 (35), 22480-22489.
8. Longo, V. D.; Gralla, E. B.; Valentine, J. S. Superoxide dismutase activity is essential for stationary phase survival in Saccharomyces cerevisiae. Mitochondrial production of toxic oxygen species in vivo. J. Biol. Chem. 1996, 271 (21), 12275-12280.
9. Pütter, J.; Becker, R. Methods of Enzymatic Analysis, 3rd ed.; Verlug Chemie: Deerfield Beach, FL, 1983; Vol. 3, pp 286-293.
10. Pluskal, M. G.; Bogdanova, A.; Lopez, M.; Gutierrez, S.; Pitt, A. M. Multiwell in-gel protein digestion and microscale sample preparation for protein identification by mass spectrometry. Proteomics 2002, 2 (2), 145-150.
11. 2H-labeled leucine. J. Mass Spectrom. Soc. Jpn. 1998, 46 (1), 83-89.
12. Pratt, J. M.; Robertson, D. H.; Gaskell, S. J.; Riba-Garcia, I.; Hubbard, S. J.; Sidhu, K.; Oliver, S. G.; Butler, P.; Hayes, A.; Petty, J.; Beynon, R. J. Stable isotope labelling in vivo as an aid to protein identification in peptide mass fingerprinting. Proteomics 2002, 2 (2), 157-163.
13. Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (17), 9390-9395.
14. Comprehensive Yeast Genome Database (CYGD) at http://mips.gsf.de/genre/ proj/yeast.
15. Futcher, B.; Latter, G. I.; Monardo, P.; McLaughlin, C. S.; Garrels, J. I. A sampling of the yeast proteome. Mol. Cell Biol. 1999, 19 (11), 7357-7368.
16. Jamieson, D. J.; Rivers, S. L.; Stephen, D. W. Analysis of Saccharomyces cerevisiae proteins induced by peroxide and superoxide stress. Microbiology 1994, 140 (Pt 12), 3277-3283.
17. Vido, K.; Spector, D.; Lagniel, G.; Lopez, S.; Toledano, M. B.; Labarre, J. A proteome analysis of the cadmium response in Saccharomyces cerevisiae. J. Biol. Chem. 2001, 276 (11), 8469-8474.
18. 35S]cysteine in the absence of cells. Anal. Biochem. 1999, 269 (1), 179-188.
19. 35S-labeled amino acids. J. Biol. Chem. 1982, 257 (17), 10400-10413.
20. Yeargin, J.; Haas, M. Elevated levels of wild-type p53 induced by radiolabeling of cells leads to apoptosis or sustained growth arrest. Curr. Biol. 1995, 5 (4), 423-431.
21. 35S-methionine inhibits cell cycle progression, proliferation, and survival. FASEB J. 2000, 14 (3), 448-454.
22. Maillet, I.; Lagniel, G.; Perrot, M.; Boucherie, H.; Labarre, J. Rapid identification of yeast proteins on two-dimensional gels. J. Biol. Chem. 1996, 271 (17), 10263-10270.
23. Meisenhelder, J.; Hunter, T. Radioactive protein-labelling techniques. Nature 1988, 335 (6186), 120.
24. McCaldon, P.; Argos, P. Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences. Proteins 1988, 4 (2), 99-122.
25. 13C- substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2003, 2 (2), 173-181.
26. Shenton, D.; Grant, C. M. Protein S-thiolation targets glycolysis and protein synthesis in response to oxidative stress in the yeast Saccharomyces cerevisiae. Biochem. J. 2003, 374 (Pt 2), 513-519.
27. Godovac-Zimmermann, J.; Brown, L. R. Perspectives for mass spectrometry and functional proteomics. Mass Spectrom. Rev. 2001, 20 (1), 1-57.
28. Pratt, J. M.; Petty, J.; Riba-Garcia, I.; Robertson, D. H.; Gaskell, S. J.; Oliver, S. G.; Beynon, R. J. Dynamics of protein turnover, a missing dimension in proteomics. Mol. Cell. Proteomics 2002, 1 (8), 579-591.
29. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1 (5), 376-386.
30. Charizanis, C.; Juhnke, H.; Krems, B.; Entian, K. D. The mitochondrial cytochrome c peroxidase Ccp1 of Saccharomyces cerevisiae is involved in conveying an oxidative stress signal to the transcription factor Pos9 (Skn7). Mol. Gen. Genet. 1999, 262 (3), 437-447.
31. Brachmann, C. B.; Davies, A.; Cost, G. J.; Caputo, E.; Li, J.; Hieter, P.; Boeke, J. D. Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 1998, 14(2), 115-132.
32. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17 (10), 994-999.
33. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. U.S.A. 2003, 100 (12), 6940-6945.
34. Hall, M. P.; Schneider, L. V. Isotope-differentiated binding energy shift tags (IDBEST) for improved targeted biomarker discovery and validation. Exp. Rev. Proteomics 2004, 1 (4), 421-431.
35. Schneider, L. V.; Hall, M. P. Stable isotope methods for high-precision proteomics. Drug Discovery Today 2005, 10 (5), 353-363.
36. Marouga, R.; David, S.; Hawkins, E. The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 2005, 382 (3), 669-678.
37. Haynes, P. A.; Yates, J. R., III. Proteome profiling-pitfalls and progress. Yeast 2000, 17 (2), 81-87.
38. Berggren, K.; Chernokalskaya, E.; Steinberg, T. H.; Kemper, C.; Lopez, M. F.; Diwu, Z.; Haugland, R. P.; Patton, W. F. Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis 2000, 21 (12), 2509-2521.
39. Unlu, M.; Morgan, M. E.; Minden, J. S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 1997, 18 (11), 2071-2077.
40. Tonge, R.; Shaw, J.; Middleton, B.; Rowlinson, R.; Rayner, S.; Young, J.; Pognan, F.; Hawkins, E.; Currie, I.; Davison, M. Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 2001, 1 (3), 377-396.
41. Zhu, H.; Pan, S.; Gu, S.; Bradbury, E. M.; Chen, X. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 2002, 16 (22), 2115-2123.
42. Ashe, M. P.; De Long, S. K.; Sachs, A. B. Glucose depletion rapidly inhibits translation initiation in yeast. Mol. Biol. Cell 2000, 11 (3), 833-848.
43. Kuhn, K. M.; DeRisi, J. L.; Brown, P. O.; Sarnow, P. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol 2001, 21 (3), 916-927.
44. Campbell, I. D.; Duffus, J. H. Yeast a Practical Approach; IRL Press: Oxford, Washington, DC, 1998.
45. Finkel, T. Oxidant signals and oxidative stress. Curr. Opin. Cell Biol. 2003, 15 (2), 247-254.
46. Madeo, F.; Frohlich, E.; Ligr, M.; Grey, M.; Sigrist, S. J.; Wolf, D. H.; Frohlich, K. U. Oxygen stress: a regulator of apoptosis in yeast. J. Cell Biol. 1999, 145 (4), 757-767.
47. Boveris, A.; Cadenas, E. Mitochondrial production of hydrogen peroxide regulation by nitric oxide and the role of ubisemiquinone. IUBMB Life 2000, 50 (4-5), 245-250.
48. Kamata, H.; Hirata, H. Redox regulation of cellular signaling. Cell. Signalling 1999, 11 (1), 1-14.
49. Holmgren, A. Thioredoxin and glutaredoxin systems. J. Biol. Chem. 1989, 264 (24), 13963-13966.
50. Minard, K. I.; McAlister-Henn, L. Antioxidant function of cytosolic sources of NADPH in yeast. Free Radical Biol. Med. 2001, 31 (6), 832-843.
51. Gasch, A. P.; Spellman, P. T.; Kao, C. M.; Carmel-Harel, O.; Eisen, M. B.; Storz, G.; Botstein, D.; Brown, P. O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 2000, 11 (12), 4241-4257.