RNA-seq analysis of E. coli BW25113 during exponential growth on M9 minimal medium supplemented with either glucose, xylose or glucose+xylose (glucose exponential phase)
Escherichia coli strain BW25113 carying the plasmid [pBR322 PihfB-mTagBFP PxylA-mRFP1] was grown on minimal M9 medium with either glucose (15 mM), xylose (18 mM), or a mix of glucose (6 mM) and xylose (11 mM). The scope here was to observe transcriptomic differences on glucose versus xylose and to pinpoint putative effects of xylose in the medium during the growth on glucose.  M9 medium contains 33.7 mM Na2HPO4, 22 mM KH2PO4, 8.55 mM NaCl, 9.35 mM NH4Cl, 1 mM MgSO4, 0.3 mM CaCl2, 13.4 mM EDTA, 3;1 mM FeCl3-6H2O, 0.62 mM ZnCl2, 76 µM CuCl2-2H2O, 42 µM CoCl2-2H2O, 162 µM H3BO3, 8.1 µM MnCl2-4H2O, 1 µg.L-1 thiamine and carbon sources as described above. M9 medium was supplemented with 20 mg.L-1 chloramphenicol to maintain the plasmid pBR322 PihfB-mTagBFP PxylA-mRFP1. This plasmid was used to slow down and monitor the glucose-xylose transition, hence it has no obvious effect on the proposed datasets since they concern exponential phases.   Growths were performed in 1L bioreactors (pH 7, 37°C, pO2>20%). Inoculations were done at 0.03 OD 600 nm and sampling was performed between OD 0.5 and 1. Three independent repetitions led to three biological replicates per conditions.  Cell samples were processed to extract RNA using trizol/phenol treatment. ERCCs were added as a control for normalization, before ribodepletion in order to eliminate ribosomal RNAs. RNAseq analysis was carried out in IonTorrent (Ion S5, Thermofischer) on the GETbiopuce platform. The data were normalized using the R package following the TMM_exact methodology developed in the team.