biostudies-arrayexpressEscherichia coli K-12https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14542Escherichia 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.biostudies-arrayexpressNucleic Acid Extraction - Cells were thawed on ice and suspended in Tris-EDTA (TE) buffer, then mechanically lysed using Fastprep (MP Biomedical) with glass beads. RNA extraction was carried out by adding Trizol and phenol. Potential DNA contamination was eliminated using the TURBO DNA-freeTM kit (Ambion). ERCC (ERCC RNA Spikes-In Control Mix 1, AMBION) was added before ribodepletion with 1 μL of ERCC diluted 1/10 for 5000 ng of total RNA. Ribodepletion was performed with the Pan-Karyote SiTools ribo POOL kit (siTOOLs Biotech).Sample Collection - 4 x 10^9 cells were centrifuged at 13,000 rpm for 2 minutes and pellets were flash frozen in liquid nitrogen.Sequencing - the 100 base pair single-end fragments were sequenced on an Ion Torrent system equipped with an Ion P1 Chip Kit by the GeT-BioPuces platform (http://get-biopuces.insa-toulouse.fr/). These experiments were repeated with three independent cultures.Library Construction - 10 ng ribodepleted RNA was used to construct a sequencing library using the Ion Total RNA-Seq Kit v2 Kit and the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Thermo Fisher Scientific, Waltham, MA, USA).Growth Protocol - Escherichia coli strain BW25113 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). 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. 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.MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesSequence Alignment - Reads were mapped onto the E. coli genome (version U0009.3, GenBank) using the Burrows-Wheeler alignment method (version 0.7.12-r1069). Counting was performed with HTSeq-count version 0.6.1p1 using the « intersection non empty » mode. Supplementary_files_format_and_content: Matrix of read counts for every gene (in total for 4488 genes)Data Transformation - Data normalization was carried out by the R package TMM_exact.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIon Torrent S5The long-held view that acetate, one of the main fermentation by-products of Escherichia coli , is toxic to microbial growth is currently challenged. Here, we demonstrate that acetate promotes E. coli adaptation to nutrient changes by accelerating growth resumption, with as little as 250 µM acetate being sufficient to shorten the lag phase by several hours. Acetate was found to be consumed via acetyl-CoA synthetase very early after the nutrient change. Transcriptomics, metabolomics and 13 C-isotope labeling experiments show that acetate replenishes metabolic pools in the tricarboxylic acid cycle and upper glycolysis. Single-cell analyses reveal that acetate increases the adaptation speed of individual cells switching to the new nutrient. We conclude that the reuse of excreted acetate by E. coli facilitates metabolic adaptation by transiently replenishing central metabolite pools. This work identifies an unexpected role of acetate in the nutritional adaptation of E. coli , providing new insights into the physiological relevance of overflow metabolism. <h4>Highlights</h4> Acetate facilitates E. coli adaptation from one nutrient to another. Less than 250 µM acetate is sufficient to halve lag times. Acetate helps replenish metabolite pools in central carbon metabolism. Acetate excretion is an adaptative strategy to overcome resource fluctuations.RNA-seq of coding RNAEscherichia coli K-12Acetate promotes Escherichia coli metabolic adaptationERP166411Brice EnjalbertLucas DEVLIN, Virginia OUDARD, Manon BARTHE, Thomas GOSSELIN-MONPLAISIR, Jean BAUDRY, Muriel COCAIGN-BOUSQUET, Pierre MILLARD and Brice ENJALBERTfalseRNA-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.2026-06-02T00:00:00Z2026-06-02T01:01:54.377Z2024-11-21T14:04:07.795ZE-MTAB-14542ERP166411EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_000418410.64898/2026.05.05.722864