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Submitted on February 23, 2006
Accepted on March 21, 2006

Gel-free and gel-based proteomics in Bacillus subtilis:A comparative study

Susanne Wolff, Andreas Otto, Dirk Albrecht, Jianru Stahl Zeng, Knut Büttner, Matthias Glückmann, Michael Hecker, and Dörte Becher

Institute of Microbiology, Ernst-Moritz-Arndt Universität, Greifswald 17489

Corresponding Author: dbecher{at}uni-greifswald.de

The proteome of exponentially growing Bacillus subtilis cells was dissected by the implementation of shotgun proteomics and a semi-gel-based approach for a particular exploration of membrane proteins. The current number of 745 protein identifications which was gained by the use of two-dimensional gel electrophoresis could be increased by 473 additional proteins. Therefore, almost 50 % of the 2500 genes expressed in growing Bacillus subtilis cells have been demonstrated at the protein level. In terms of exploring cellular physiology and adaptation to environmental changes or stress, proteins showing an alteration in expression level are of primary interest. The large number of vegetative proteins identified by the gel-based and gel-free approach is a good starting point for comparative physiological investigations. For this reason a gel-free quantitation with the recently introduced iTRAQ reagent technique was performed to investigate the heat shock response in Bacillus subtilis. A comparison with gel-based data showed that both techniques revealed a similar level of upregulation for proteins belonging to well studied heat hock regulons (SigB, HrcA and CtsR). However, additional datasets have been obtained by the gel-free approach indicating a strong heat sensitivity of specific enzymes involved in amino acid synthesis.


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