Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress

Institut für Mikrobiologie und Molekularbiologie, Ernst-Moritz-Arndt-Universität Greifswald, D-17487 Greifswald, Germany Correspondence Georg Homuth georg.homuth{at}uni-greifswald.de The Gram-positive soil bacterium Bacillus subtilis responds to oxidative stress by the activation of different cellular defence mechanisms. These are composed of scavenging enzymes as well as protection and repair systems organized in highly sophisticated networks. In this study, the peroxide and the superoxide stress stimulons of B. subtilis were characterized by means of transcriptomics and proteomics. The results demonstrate that oxidative-stress-responsive genes can be classified into two groups. One group encompasses genes which show similar expression patterns in the presence of both reactive oxygen species. Examples are members of the PerR and the Fur regulon which were induced by peroxide and superoxide stress. Similarly, both kinds of stress stimulated the activation of the stringent response. The second group is composed of genes primarily responding to one stimulus, like the members of the SOS regulon which were particularly upregulated in the presence of peroxide, and many genes involved in sulfate assimilation and methionine biosynthesis which were only induced by superoxide. Several genes encoding proteins of unknown function could be assigned to one of these groups. Abbreviations: 2D, two-dimensional; MALDI-TOF-MS, matrix-associated laser desorption ionization time of flight mass spectrometry; ROS, reactive oxygen species J. Mostertz and C. Scharf contributed equally to this work. The datasets for all genes significantly up- and downregulated by peroxide and paraquat stress including all expression level ratios are available as supplementary data with the online version of this paper at http://mic.sgmjournals.org . The complete dataset of the transcriptome analysis can be obtained from the authors upon request.