Transcriptome analysis of C. glutamicum ΔaceE Δpyc versus ΔaceE

The pyruvate dehydrogenase complex (PDHC) catalyzes the oxidative decarboxylation of pyruvate yielding acetyl-CoA and CO2. The PDHC-deficient Corynebacterium glutamicum strain ΔaceE is therefore lacking an important decarboxylation step in central metabolism. Additional inactivation of pyc, encoding pyruvate carboxylase, resulted in a >15 hour lag phase in the presence of glucose, while no growth defect was observed on gluconeogenetic substrates like acetate. Transcriptome analysis as well as an adaptive laboratory evolution experiment of strain ΔaceE Δpyc revealed the reduction of glucose uptake as a key adaptive measure to enhance growth on glucose/acetate mixtures. For analysis of the transcriptome, C. glutamicum ΔaceE and ΔaceE Δpyc were cultivated in triplicates in 50 ml CGXII containing 154 mM acetate and 222 mM glucose in shake flasks. After reaching exponential phase at an OD600 of around 12-15, the cell suspension was harvested by centrifugation (4256 g, 10 min, 4°C). The resulting pellet was directly frozen in liquid nitrogen and stored at -80°C. RNA preparation, cDNA synthesis as well as microchip hybridization, scanning and data analysis.