Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli

DNA microarray technology was applied to detect differential transcription profiles of a subset of the Escherichia coli genome. A total of 111 E. coli genes, including those in central metabolism, key biosyntheses, and some r egulatory functions, were cloned, amplified, and used as probes for detecti ng the level of transcripts. An E. coli strain was grown in glucose, acetat e, and glycerol media, and the transcript levels of the selected genes were detected. Despite extensive studies on E. coli physiology, many new featur es were found in the regulation of these genes. For example, several genes were unexpectedly up-regulated, such as pps, ilvG, aroF, secA, and dsbA in acetate and asnA and asnB in glycerol, or down-regulated, such as ackA, pta , and adhE in acetate. These genes were regulated with no apparent reasons by unknown mechanisms. Meanwhile, many genes were regulated for apparent pu rposes but by unknown mechanisms. For example, the glucose transport genes (ptsHI, ptsG, err) in both acetate and glycerol media were down-regulated, and the ppc, glycolytic, and biosynthetic genes in acetate were also down-r egulated because of the reduced fluxes. However, their molecular mechanisms remain to be elucidated. Furthermore, a group of genes were regulated by k nown mechanisms, but the physiological roles of such regulation remain uncl ear. This group includes pckA and aspA, which are up-regulated in glycerol, and gnd and aspA, which are down- and up-regulated, respectively, in aceta te. The DNA microarray technology demonstrated here is a powerful yet econo mical tool for characterizing gene regulation and will prove to be useful f or strain improvement and bioprocess development.