Analysis of global responses by protein and peptide fingerprinting of proteins isolated by two-dimensional gel electrophoresis. Application to the sulfate-starvation response of Escherichia coli

European Journal of Biochemistry

Volumn 239, Issue 3, 1996, Pages 773-781

  Quadroni, Manfredo ^a   Staudenmann, Werner ^a   Kertesz, Michael ^a   James, Peler ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Database; Electrophoresis; Mapping; Mass spectrometry

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INDUCTION; PROTEIN ISOLATION; STARVATION; TECHNIQUE; TWO DIMENSIONAL ELECTROPHORESIS;

BACILLUS SUBTILIS; ESCHERICHIA COLI;

EID: 0030003403     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.1996.0773u.x     Document Type: Article

References (35)

1. Adams, M. D., Kelley, J. M., Gocayne J. D., Dubnik, M., Polymeropoulus. M. H., Xiao, H., Merril, M., Wu, A., Olde, B., Moreno, R. F., Kerlavage, A. R., McCombie, W. R. & Venter, J. C. (1991) Complementary DNA sequencing: expressed sequence tags and human genome project, Science 252, 1651-1656.
2. Aebersold, R. H., Leavitt, J., Saavedra, R. A., Hood, L. E. & Kent, S. B. (1987) Internal amino acid sequence analysis of proteins separated by one- or two-dimensional gel electrophoresis after in situ protease digestion on nitrocellulose, Proc. Natl Acad. Sci. USA 84, 6970-6974.
3. Appel, R. D., Hochstrasser, D. F. Funk, M., Vargas, J. R., Pellegrini, C., Muller, A. F. & Schemer, J. R. (1991) The MHLANIE project: from a biopsy to automatic protein map interpretation by computer, Electrophoresis 12, 722-735.
4. Beil, S., Kehrli, H., James, P., Staudenmann, W., Cook, A. M., Leisinger, T. & Kerlesz, M. A. (1995) Purification and characterization of the arylsulphatase synthesised by Pseudomonas aeruginosa PAO during growth in sulfate-free medium and cloning of the arylsulphatase gene (atsA), Eur. J. Biochem. 229, 385-394.
5. Biemunn, K. (1988) Contributions of mass spectrometry to peptide and protein structure, Biomed. Environ. Mass Spectrom. 16, 99-111.
6. Butler, J. D., Levin, S. W., Facchiano, A., Miele, L. & Mukherjee, A. B. (1993) Amino acid composition and N-terminal sequence of purified cystine binding protein of Escherichia coli, Life Sci. 52, 1209-1215.
7. Eng, J. K., McCormack, A. L. & Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database, J. Am. Soc. Mass Spectrom. 5, 976-989.
8. Henzel, W., Billeci, T., Stults, J., Wong, S., Grimley, C. & Watanabe, C. (1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases, Proc. Natl Acad. Sci. USA 90, 5011-5015.
9. Hochstrasser, D. F., Harrington, M. G., Hochstrasser, A.-C., Miller, M. J. & Merril, C. R. (1988) Methods for increasing the resolution of two dimensional protein electrophoresis. Anal. Biochem. 173, 424-435.
10. Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S. & Hauer, C. R. (1986) Protein sequencing by tandem mass spectrometry. Proc. Natl Acad. Sci. USA 83, 6233-6237.
11. Jacobson, B. L., He, J. J., Vermersch, P. S., Lemon, D. D. & Quiocho, F. A. (1991) Engineered interdomain disulfide in the periplasmic receptor for sulfate transport reduces flexibility. Site-directed mutagenesis and ligand-binding studies, J. Biol. Chem. 266, 5220-5225.
12. James, P., Quadroni, M., Carafoli, E. & Gonnet, G. (1993). Protein identification by mass profile fingerprinting, Biochem. Biophys. Res. Commun. 195, 58-64.
13. James, P., Quadroni, M. Carafoli, K. & Gonnet, G. (1994) Protein identification in DNA databases by peptide mass fingerprinting, Protein Sci. 3, 1347-1350.
14. Kertesz, M. A., Leisinger, T. & Cook, A. M. (1993) Proteins induced by sulfate limitation in Escherichia coli, Paeudomonas putida or Staphylococcus aureus, J. Bacteriol. 175, 1187-1190
15. Levy, S. & Danchin, A. (1988) Phylogeny of metabolic pathways: O-Acetylserine acetylhydrolase A is homologous to the tryptophan synthase beta subunit, Mol. Microbiol. 2, 777-783.
16. Mann, M., Hojrup, P. & Roepstorff, P. (1993) Use of mass spectrometric molecular mass information to identify proteins in sequence databases, Biol. Mass Spectrom. 22, 338-345.
17. Mann, M. & Wilm, M. (1994) Error-tolerant identification of peptides in sequence databases by peptide sequence tags, Anal. Chem. 66, 4390-4399.
18. Mytelka, M. & Chamberlin, M. J. (1996) Escherichia coli fliA2Y operon, J. Bacteriol. 178, 24-34.
19. O'Farrell, P. H. (1975) High resolution two-dimensional electroporesis of proteins, J. Biol. Chem. 250, 4007-4021.
20. Pappin, D., Hojrup, P. & Bleasby, A. (1993) Rapid identification of proteins by peptide-mass fingerprinting, Current Biol. 3, 327-332.
21. Pearson, W. R. & Lipman, D. J. (1988) Improved tools for biological sequence comparison, Proc. Natl Acad. Sci. USA 85, 2444-2448.
22. Piceinni, E., Staudenmann, W., Albergoni, V., De Gabrieli, R. & James, P. (1994) Purification and primary structure of metallothioneins induced by cadmium in the protists Tetrahymena pigmentosa and Tetrahymena pyriformis, Eur. J. Biochem. 226, 853-859.
23. Quadroni, M., James, P. & Carafoli, E. (1994) Isolation of phosphorylated calmodulin from rat liver and identification of the in vivo phosphorylation sites, J. Biol. Chem. 269, 16116-16122.
24. Rasmussen, H. H., Mortz, E., Mann, M., Roepstorff, P. & Celis, J. E. (1994) Identification of transformation sensitive proteins recorded in human two-dimensional gel protein databases by mass sepctrometric peptide mapping alone and in combination with microsequencing, Electrophoresis 15, 406-416.
25. Roepstorff, P. & Fohlman, J. (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides, Biomed. Environ. Mass Spectrom. 11, 601-603.
26. Schagger, H. & von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa, Anal. Biochem. 166, 368-379.
27. Silhavy, T. J., Berman, M. L. & Enquist, L. W. (1984) Experiments with gene fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor.
28. Smillie, D. A., Hayward, R. S., Suzuki, T., Fujita, N. & Ishihama, A. (1992) Locations of genes encoding alkyl hydroperoxide reductase on the physical map of the Escherichia coli K-12 genome, J. Bacterioi. 174, 3826-3827.
29. Taylor, J., Anderson, N. L., Scandora, A. E., Villard, K. E. & Anderson, N. G. (1982) The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns, Clin. Chem. 28, 861-866.
30. Torriani-Gorini, A. (1994) The Pho regulon of Escherichia coli, in Phosphate in microorganisms (Torriani-Gorini, A., Yagil, E. & Silver, S., eds) pp. 1-4, ASM Press, Washington.
31. Wilm, M., Shevehenko, A., Houthaeve, T., Breit, S., Schweigerer, L., Fotsis, T. & Mann, M. (1996) Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry, Nature 379, 466-469.
32. Yates, J. R., Speicher, S., Griffin, P. R. & Hunkapillar, T. (1993) Peptide mass maps - A highly informative approach to protein identification, Anal. Biochem. 214, 397-408.
33. Yates, J. R., Eng, J. K., McCormack, A. L. & Sehieltz, D. (1995) A method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database, Anal. Chem. 67, 1426-1436.
34. Van Bogelen, R. A., Sankar, P., Clark, R. L., Bogan, J. A. & Neidhardt, F. C. (1992) The gene-protein database of Escherichia coli, edition 5, Electrophoresis 13, 1014-1054.
35. Vandekerckhove, J., Bauw, G., Puype, M., Van Damme, J. & Van Montagu, M. (1985) Protein-blotting on Polybrene-coated glass-fiber sheets, Eur. J. Biochem. 152, 9-19.