The two-phase partitioning system - a powerful technique to purify integral membrane proteins of Corynebacterium glutamicum for quantitative shotgun analysis

Proteomics

Volumn 9, Issue 8, 2009, Pages 2263-2272

  Fränzel, Benjamin ^a   Fischer, Frank ^a   Trötschel, Christian ^a   Poetsch, Ansgar ^a   Wolters, Dirk ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

Biphasic partitioning system; Corynebacterium glutamicum I Gram positive bacteria; Membrane proteome; MudPIT

Indexed keywords

BACTERIAL PROTEIN; INTEGRAL MEMBRANE PROTEIN; NITROGEN 15; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL MEMBRANE; CONTROLLED STUDY; CORYNEBACTERIUM GLUTAMICUM; ISOTOPE LABELING; NONHUMAN; PHASE PARTITIONING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PURIFICATION; PROTEIN TRANSPORT; QUANTITATIVE ANALYSIS;

BACTERIAL PROTEINS; CELL MEMBRANE; CHEMICAL FRACTIONATION; CORYNEBACTERIUM GLUTAMICUM; MEMBRANE PROTEINS; PROTEOME; SUBCELLULAR FRACTIONS; TANDEM MASS SPECTROMETRY;

CORYNEBACTERIUM GLUTAMICUM; POSIBACTERIA;

EID: 65349126971     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800766     Document Type: Article

References (28)

1. Liebl, W., in: Balows, A., Trueper, H. G., Dworkin, M., Harder, W., Schleifer, K.-H. (Eds.), The Prokaryotes, Springer, New York 1992, pp. 1157-1171.
2. Peyret, J. L, Bayan, N., Joliff, G., Gulik-Krzywicki, T. et al., Characterization of the cspB gene encoding PS2, an ordered surface-layer protein in Corynebacterium glutamicum. Mol. Microbiol. 1993, 9, 97-109.
3. Bayan, N., Houssin, C., Chami, M., Leblon, G., Mycomembrane and S-layer: Two important structures of Corynebacterium glutamicum cell envelope with promising biotechnology applications. J. Biotechnol. 2003, 104, 55-67.
4. Hermann, T., Finkemeier, M., Pfefferle, W., Wersch, G. et al., Two-dimensional electrophoretic analysis of Corynebacterium glutamicum membrane fraction and surface proteins. Electrophoresis 2000, 21, 654-659.
5. Klein, C., Garcia-Rizo, C., Bisle, B., Scheffer, B. et al., The membrane proteome of Halobacterium salinarum. Proteomics 2005, 5, 180-197.
6. Fischer, F., Wolters, D., Rogner, M., Poetsch, A., Toward the complete membrane proteome: High coverage of integral membrane proteins through transmembrane peptide detection. Mol. Cell. Proteomics 2006, 5, 444-453.
7. Wolters, D. A., Washburn, M. P., Yates, J. R., Ill, An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 2001, 73, 5683-5690.
8. Schindler, J., Nothwang, H. G., Aqueous polymer two-phase systems: Effective tools for plasma membrane proteomics. Proteomics 2006, 6, 5409-5417.
9. Persson, A., Jergil, B., The purification of membranes by affinity partitioning. FASEB J. 1995, 9, 1304-1310.
10. Cao, R., Li, X., Liu, Z., Peng, X. et al., Integration of a twophase partition method into proteomics research on rat liver plasma membrane proteins. J. Proteome Res. 2006, 5, 634- 642.
11. Everberg, H., Peterson, R., Rak, S., Tjerneld, F., Emanuelsson, C., Aqueous 2wo-phase partitioning for proteomic monitoring of cell surface biomarkers in human peripheral blood mononuclear cells. J. Proteome Res. 2006, 5, 1168- 1175.
12. MacCoss, M. J., Wu, C. C., Liu, H., Sadygov, R., Yates, J. R., Ill, A correlation algorithm for the automated quantitative analysis of shotgun proteomics data. Anal. Chem. 2003, 75, 6912-6921.
13. Koch, D. J., Ruckert, C., Rey, D. A., Mix, A. et al., Role of the ssu and seu genes of Corynebacterium glutamicum ATCC 13032 in utilization of sulfonates and sulfonate esters as sulfur sources. Appl. Environ. Microbiol. 2005, 71, 6104- 6114.
14. Schluesener, D., Rogner, M., Poetsch, A., Evaluation of two proteomics technologies used to screen the membrane proteomes of wild-type Corynebacterium glutamicum and an L-lysine-producing strain. Anal. Bioanal. Chem. 2007, 389, 1055-1064.
15. Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N. et al., The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L- aspartate-derived amino acids and vitamins. J. Biotechnol. 2003, 104, 5-25.
16. Tabb, D. L, McDonald, W. H., Yates, J. R., Ill, DTASelect and contrast: Tools for assembling and comparing protein identifications from shotgun proteomics. J. Proteome Res. 2002, 7, 21-26.
17. Pan, C., Kora, G., McDonald, W. H., Tabb, D. L. et al., ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation. Anal. Chem. 2006, 78, 7121-7131.
18. Eng, J. K., McCormack, A. L., Yates, J. R., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
19. Zybailov, B., Coleman, M. K., Florens, L., Washburn, M. P., Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal. Chem. 2005, 77, 6218-6224.
20. Monsigny, M., Petit, C., Roche, A. C., Colorimetric determination of neutral sugars by a resorcinol sulfuric acid micromethod. Anal. Biochem. 1988, 175, 525-530.
21. Schluesener, D., Fischer, F., Kruip, J., Rogner, M., Poetsch, A., Mapping the membrane proteome of Corynebacterium glutamicum. Proteomics 2005, 5, 1317-1330.
22. McHardy, A. C., Puhler, A., Kalinowski, J., Meyer, F., Comparing expression level-dependent features in codon usage with protein abundance: An analysis of 'predictive proteomics'. Proteomics 2004, 4, 46-58.
23. Washburn, M. P., Wolters, D., Yates, J. R., Ill, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19, 242- 247.
24. Xiong, Y, Chalmers, M. J., Gao, F. P., Cross, T. A., Marshall, A. G., Identification of Mycobacterium tuberculosis H37Rv integral membrane proteins by one-dimensional gel electrophoresis and liquid chromatography electrospray ionization tandem mass spectrometry. J. Proteome Res. 2005, 4, 855-861.
25. Poetsch, A., Wolters, D., Bacterial membrane proteomics. Proteomics 2008, 8, 4100-4122.
26. Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. L., Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 2001,305, 567-580.
27. Baumbach, J., CoryneRegNet 4.0-A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007, 8, 429.
28. Weinand, M., Kramer, R., Morbach, S., Characterization of compatible solute transporter multiplicity in Corynebacterium glutamicum. Appl. Microbiol. Biotechnol. 2007, 76, 701- 708.