Proteomics, DNA arrays and the analysis of still unknown regulons and unknown proteins of Bacillus subtilis and pathogenic Gram-positive bacteria

The complete sequence of the bacterial genomes provides new perspectives fo r the study of gene expression and gene function. By the combination of the highly sensitive 2-dimensional (2D) protein gel electrophoresis with the i dentification of the protein spots by microsequencing or mass spectrometry we established a 2D protein index of Bacillus subtilis that currently compr ises almost 400 protein entries. A computer-aided evaluation of the 2D gels loaded with radioactively-labelled proteins from growing or stressed/starv ed cells proved to be a powerful tool in the analysis of global regulation of the expression of the entire genome. For the general stress regulon it is demonstrated how the proteomics approa ch can be used to analyse the regulation, structure and function of still u nknown regulons. The application of this approach is illustrated for the si gma(B) dependent general stress regulon. For the comprehensive description of proteins/genes belonging to stimulons or regulons it is generally recomm ended to complement the proteome approach with DNA array techniques in orde r to identify and allocate still undiscovered members of individual regulon s. This approach is also very attractive to uncover the function of still u nknown global regulators and regulons and to dissect the entire genome into its basic modules of global regulation. The same strategy can be used to a nalyse the regulation, structure and function of regulons encoding virulenc e factors of pathogenic bacteria for a comprehensive understanding of the p athogenicity and for the identification of new antibacterial targets.