Transcriptome analysis of genome-reduced Bacillus subtilis strains

In this study two genome-reduced Bacillus subtilis strains lacking about 36% of dispensable genetic information were constructed using a markerless and scarless deletion method. In order to analyze the consequences of the deletions for the bacteria, a multi-omics characterization of the reference strain Δ6 (Westers et al., 2003; PMID 12949151) and the two deletion strains was carried out. Bacteria were cultivated in complex medium supplemented with glucose, and samples of the same cultures were subjected to metabolome, proteome, and transcriptome analyses.These revealed a massive re-organization of metabolism as well as substantial changes in the transcriptome and the proteome. Global gene expression changes between the reference strain Δ6 and the deletion strains PG10 and PS38, grown to mid-exponential phase in LB medium supplemented with glucose, were examined using whole-genome tiling arrays. Hybridizations were performed in quadruplicate using RNA isolated from independent cultures.