Systemic post-translational control of bacterial metabolism regulates adaptation in dynamic environments

E. coli K-12 MG1655 was grown on M9 minimal media supplemented with 0.2% w/v glucose, fructose, or acetate. The goal of this study was to determine differentially expressed genes in the different media conditions. Gene expression profiling data were generated from cultures of exponentially-growing E. coli under aerobic conditions on glucose, fructose, or acetate M9 minimal media. E. coli K12 MG1655 was grown and expression profiled on 0.2% (w/v) glucose M9 minimal media or 0.2% (w/v) fructose M9 minimal media or 0.2% (w/v) acetate M9 minimal media at 37°C. Expression profiling was done using Affymetrix E. coli Genome 2 Arrays. Each experimental condition was tested in triplicate in the respective carbon sources using independent cultures and processed following the manufacturer-recommended protocols. Cultures were grown to mid-exponential growth phase aerobically (OD600 = 0.3) in minimal media, supplemented with the appropriate carbon source. Three ml of culture was added to 2 volumes of RNAprotect Bacteria Reagent (Qiagen) and total RNA was then isolated using RNeasy columns (Qiagen) with DNase I treatment. cDNA synthesis, fragmentation, end-terminus biotin labeling, and array hybridization were performed as recommended by the Affymetrix standard protocol.