Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate

DNA microarray was used to study the transcription profiling of Escherichia coli adapting to acetate as a sole carbon source. Bacteria grown in glucose minimal media were used as a reference. The dynamic expression levels of 3,497 genes were monitored at seven time points during this adaptation. Among the central metabolic genes, the glycolytic and glucose phosphotransferase genes were repressed as the bacteria entered stationary phase, whereas the glyoxylate pathway, TCA cycle, and gluconeogenic genes were induced. Distinct induction or repression patterns were recognized among different pathway genes. For example, the repression of glycolytic genes and the induction of gluconeogenic ones started immediately after glucose was depleted. On the other hand, the regulation of the pentose phosphate pathway genes and glyoxylate genes gradually responded to the glucose depletion or was more related to growth in acetate. When the whole genome was considered, many of the CRP, FadR, and Cra regulons were immediately responsive to the glucose depletion, whereas the σ^s, Lrp, and IHF regulons were gradually responsive to the glucose depletion. The expression profiling also provided differential regulations between isoenzymes; for example, malic enzymes A (sfcA) and B (maeB). The expression profiles of three genes were confirmed with RT-PCR.