From the LC-MS/MS data of 52 SDS-PAGE slices, 4,333 peptides from 948 proteins were identified (see the additional file 1) with a false discovery rate of 6.75% of the peptide level (BI 6727 order Figure 2). During the diauxie, we observed rapid changes in protein expression (see the additional

file 2). However the magnitude of those changes was not as drastic as gene expression. Comparing with the publicly available gene expression data from Traxler et al. [13], many similar expression patterns can be recognized, especially for strongly upregulated genes/proteins. Not surprisingly, selleck inhibitor β-galactosidase expression increased strongly, almost 16-fold, during diauxic shift and followed the dynamics of gene expression (Figure 3) with a small lag expected by the delay between NVP-BGJ398 solubility dmso gene activation and accumulated protein. The genetic response occurred immediately after glucose exhaustion but protein synthesis is typically delayed between 20 seconds and several minutes in E. coli [3]. Small relative changes in concentration of already abundant proteins are difficult to detect immediately

and need to be accumulated for some time before they can be observed. Nevertheless, we noticed that the most significant changes in protein abundance took place within 40 minutes after onset of diauxic shift, which is consistent with published gene expression data and the observed resuming of growth. Since the gene expression data was derived from that published by Traxler et al., the alignments of the time-scales are not perfect and minor discrepancies between the sampling of the gene and protein expression could be expected. The protein expression measurements were with a few Thymidylate synthase exceptions reproducible, albeit not always in perfect agreement with the published gene expression data. This could be explained by noise in the data and the fact that gene and protein expression were not measured in the same cell culture. For instance, the change in gene expression of malE is almost the same as for lacZ, but at the

proteomic level we observed only slight changes in abundance of the maltose-binding protein coded for by malE (Figure 3). (The maltose-binding protein is a periplasmic component of the maltose ABC transporter which is capable of transporting malto-oligosaccharides up to seven glucose units long [16].) Figure 1 Measured cell growth and glucose concentration. Measured cell growth (OD600, blue) and glucose concentration (red) in one glucose-lactose diauxie experiment. The onset of the diauxic shift is easily determined from the 20-30 minute plateau in the growth curve, which coincides with the depletion of glucose in the medium. After about +200 minutes, both sugars are exhausted and the growth stops (OD600max = 2.2-2.4). Figure 2 Glucose-lactose diauxie protein expression. The proteins expressions were visualized using R and clustered in three groups (green – upregulated, red – downregulated, gray – no change).