biostudies-arrayexpressBrice EnjalbertEscherichia coli K-12https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16650This experiment was performed to challenge E. coli response to acetate when switched from N-Acetyl Glucosamine (NAG) to malate as the main substrate. Here, E. coli BW25113 strain was grown in M9 medium complemented with 15 mM NAG, The cells were grown to mid-exponential phase in shake flasks at 37 °C and 200 rpm before being switched to either 25 mM malate or 25 mM Malate plus 3mM Acetate. After 30 min on the new medium, sampling was perform before proceeding to RNA extraction and subsequent microarray analysis. Five biological replicates were analyzed for each condition. We thank all the INSA-Toulouse students that participated in this project: Eva Antico, Tristan Baeumlin, Camille Dessemond, Esteban Duneau, Margot Duhamel, Hermeline Frenoy, Florian Jabally, Emma Landolt, Lorenzo Molinengo, Océane Renard, Zawata-Afnan Sharara and Julie Souloumiac.biostudies-arrayexpressNucleic Acid Extraction - The RNA isolation was performed by Qiagen RNeasy Mini Kit following the instructions. RNA concentrations were measured by ND 1000 Nanodrop (Thermo Fisher), and the RNA quality was checked by capillary electrophoresis (2100 Bioanalyzer from Agilent, Santa Clara, California, USA) in accordance with the manufacturers instructions.Scaning - The slide was scanned on a Tecan MS200 scanner. The median signal of each spot in the hybridized arrays was determined and quantified using Feature Extraction software v11.5.1.1. The images were analysed with the DEVA 1.2.1 software. All array procedures were performed by the GeT-Biopuces platform (http://get.genotoul.fr/).Hybridization - RNAs hybridization on an eight-zone chip was performed and the chip was placed for 17 hours at 65°C. Then, the gene expression levels were measured by the One-Color Microarray-Based Gene Expression Analysis protocol from Agilent Technologies. The hybridization step was carried out with a microarray from Agilent (E. coli microarray slides, Alberta University, Edmonton, Alberta, Canada). The microarray slide was washed, then scanned with MS200 scanner from Tecan.Growth Protocol - The strain used in this study was wild-type Escherichia coli K-12 BW25113. The growth experiments were carried out in M9 minimum medium (Na2HPO4,12H2O 9.2mM; KH2PO4 4.4 mM; NaCl 8.6 mM; NH4Cl 38.1 mM; MgSO4 0.2 M; CaCl2 10 mM; Na2EDTA,2H2O 0.040 mM; ZnSO4,7H2O 0.015 mM; CoCl2,6H2O 1.3 μM; MnCl2,4H2O 5.1 μM; H3BO3 16.2 μM; NaMoO4,2H2O 1.65 μM; FeSO4,7H2O 10.79 μM; CuSO4,5H2O 1.20 μM; thiamine hydrochloride 29,6 mM) supplemented with 15 mM N Acetyl Glucosamine. E. coli cells were thawed and grown overnight in 50 ml preculture M9 medium. From this preculture, cultures were performed in 250 ml Erlenmeyer flask, with 15 mM NAG ate 0D 600 nm = 0.1. Once the culture reach OD = 1, cells were switched to 50 ml of M9 minimum medium plus 25 mM Malate or 25 mM Malate + 3 mM Acetate. These flasks were incubated at 37°C, with a 220 rpm shaking (Ivymen System shaking incubator, reference AG079). OD was measured at wavelength of 600 nm using a spectrophotometer (Genesys 10S UV-VIS spectrophotometer from Thermo Scientific). RNA Sampling was performed after 30 min, before growth resuming. Cultures were followed over 8 hours of growth.Sample Collection - At the end of the culture, 4 x 10^9 cells were centrifuged at 13,000 rpm for 2 minutes and pellets were flash frozen in liquid nitrogen.Labeling - Samples were diluted to obtain 100 ng of RNA in a final volume of 2.5 µl. This volume was mixed with 2 µl of Spike and 0.8 µl of random primer. Spike, an internal control of the One colour Microarray-Based Gene Expression Analysis (Agilent Technologies), is constituted by small virus RNA sequences of variable sizes and concentrations. It efficiently allows monitoring microarray workflow for linearity, sensitivity and accuracy. Then, this mix was denatured at 65°C for 10 minutes and kept on ice for 5 minutes. The reverse transcription was performed using the AffinityScript One-Step RT-PCR Kit (Agilent Technologies), at 40°C for 2 hours and at 70°C for 15 minutes. These cDNA are transcribed into cRNA using the One-Color Microarray-Based Gene Expression Analysis from Agilent Technologies.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsData Transformation - Only the signals corresponding to strain MG1655 were treated. To remove differences in labelling intensity, each raw data set was normalized on its median value. This normalized data are provided as \"Processed\" text files. Since there were 5 sets for each conditions, average values of the intensity were calculated for each gene in each condition. Relative values were obtained by dividing gene value by their value in the control without addition of acetate.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsThe 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.transcription profiling by arrayEscherichia coli K-12Acetate promotes metabolic adaptation of Escherichia coliBrice EnjalbertLucas DEVLIN, Virginia OUDARD, Manon BARTHE, Thomas GOSSELIN-MONPLAISIR, Jean-Baptiste DUPIN, Florence CONDAMINE, Jean BAUDRY, Muriel COCAIGN-BOUSQUET, Pierre MILLARD and Brice ENJALBERTfalseEffect of acetate during Escherichia coli switch from N-Acetyl Glucosamine to MalateThis experiment was performed to challenge E. coli response to acetate when switched from N-Acetyl Glucosamine (NAG) to malate as the main substrate. Here, E. coli BW25113 strain was grown in M9 medium complemented with 15 mM NAG, The cells were grown to mid-exponential phase in shake flasks at 37 °C and 200 rpm before being switched to either 25 mM malate or 25 mM Malate plus 3mM Acetate. After 30 min on the new medium, sampling was perform before proceeding to RNA extraction and subsequent microarray analysis. Five biological replicates were analyzed for each condition. We thank all the INSA-Toulouse students that participated in this project: Eva Antico, Tristan Baeumlin, Camille Dessemond, Esteban Duneau, Margot Duhamel, Hermeline Frenoy, Florian Jabally, Emma Landolt, Lorenzo Molinengo, Océane Renard, Zawata-Afnan Sharara and Julie Souloumiac.2026-05-12T00:00:00Z2026-05-14T01:01:40.476Z2026-02-13T11:51:37.412ZE-MTAB-16650EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0005518EFO_0003816EFO_000381510.64898/2026.05.05.722864