To understand both the complex structure and behavior of signal transduction and regulation in bacterial cells requires an overall holistic approach. Due to the multitude of interacting components an understanding of these processes just by reflection is not possible. Here, the aid of mathematical modeling is absolutely essential to confirm the available biological knowledge by system theoretical analysis. Two examples of a global regulatory system, namely catabolite repression in Escherichia coli and redox control in Rodospirillum rubrum are discussed and compared. The regulation of stress sigma factor sigma(S) in E. coli is then dealt with as an example of regulated gene expression combined with proteolysis. Finally, phototaxis in Halobacterium salinarum is considered as a representative of a bacterial signal transduction system. Important questions are related to the modularity and the hierarchical structure of these systems. The goal is to decompose a signaling or regulatory system into components of elementary signal transfer and to discover common features of there systems. (c) 2006 Elsevier Ltd. All rights reserved.