Transcriptome analysis of Bacillus subtilis salt stress adaptation

Whole-genome microarray technology and state-of-the-art proteomic techniques were applied to provide a global and time-resolved picture of the physiological response of B. subtilis cells exposed to a severe and sudden osmotic up-shift. This combined experimental approach provided quantitative data for 3961 mRNA profiles, 590 expression profiles of proteins detected in the cytosol and 383 expression profiles of proteins detected in the membrane fraction. Our study uncovered a well-coordinated induction of gene expression subsequent to an osmotic up-shift that involves large parts of the SigB, SigW, SigM and SigX regulons and additionally osmotic up-regulation of a large number of genes that do not belong to these regulons. In total, osmotic up-regulation of about 500 B. subtilis genes was observed. Our data provide an unprecedented rich basis for further in-depth investigation on the physiological and genetic responses of B. subtilis to hyperosmotic stress. Cells were grown in a minimal medium to early exponential phase and were then exposed to a strong osmotic up-shift by the addition of 6% (w/v) NaCl. Samples were taken before and 10, 30, 60 and 120 min subsequent to the addition of NaCl. Microarray hybridizations were performed with RNA from three biological replicates. The individual samples were labeled with Cy5; a reference pool consisting of equal amounts of RNA from all 15 samples was labeled with Cy3 (common reference design). After intensity-dependent (Lowess) normalization, the ratios of duplicate spots were averaged resulting in three biologically independent expression values per gene and time point.