Transcriptome analysis of glucose starved Bacillus subtilis cells

In this study, temporal changes in the proteome, transcriptome and extracellular metabolome of B. subtilis caused by glucose starvation were monitored. For proteomic profiling, a combination of in vivo metabolic labeling and shot gun mass spectrometric analysis was carried out for five different proteomic subfractions (i. cytosolic, ii. extracellular, iii. membrane, iv. integral membrane, and v. surface proteome fraction) leading to the identification of about 52% of the predicted proteome of B. subtilis. Acquired proteomic and transcriptomic data were analyzed using Voronoi treemaps which link functional classifications and relative expression changes of gene products according to their fate in the stationary phase. The data obtained enables for in-depth analysis of major physiological processes including protein degradation and is the first comprehensive profiling of changes in the membrane subfraction. Cells were grown in a minimal medium with glucose and L-malate (0.05 % each) to induce glucose starvation after growth to an OD500 of 1.0. Samples were taken at different time points along the growth curve (exponential growth, transition phase, transition phase +30, +60 and +120 minutes). Microarray hybridizations were performed with RNA from two biological replicates. The individual samples were labeled with Cy5; a reference pool containing equal amounts of RNA from all 10 samples was labeled with Cy3.