biostudies-arrayexpressZainab EdooMycobacterium tuberculosishttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16253Alpibectir potentiates the activity of ethionamide and prothionamide, which are second-line antibiotics used for tuberculosis treatment. Both are prodrugs whose antibacterial activity depends on bioactivation by oxidases, including the Baeyer-Villiger monooxygenase MymA. Alpibectir binds the transcriptional regulator VirS, increasing MymA expression and potentiating Eto and Pto activity. To determine the transcriptional response of M. tuberculosis to alpibectir, we treated cultures at an optical density of 0.7 with alpibectir 0.1 mg/L for 24 h. Alternatively, we determined the transcriptional response of cultures first treated with alpibectir 0.1 mg/L for 20 h followed by ethionamide 2 mg/L for 4 h. Untreated controls (DMSO 0.1%) were included.biostudies-arrayexpressSample Collection - 10 mL of the treated and control cultures were harvested by centrifugation at 3,000 x g for 5 min.Library Construction - Libraries for Illumina sequencing were prepared with the TruSeq RNA sample preparation kit version 2.0 rev. A (Illumina Inc.). All cDNA libraries were uniquely indexed.Sequencing - cDNA libraries were sequenced using an Illumina NextSeq 500 system (Illumina Inc.) in high-output mode. All samples were multiplexed on one lane of the flow cell and sequenced in single-read sequencing mode with read lengths of 150 bp.Growth Protocol - 25 mL cultures were grown at 37°C without agitation to an optical density at 600 nm of 0.7.Sample Treatment - Individual cultures at an optical density of 0.7 were treated with alpibectir 0.1 mg/L alone for 24 h or with alpibectir 0.1 mg/L for 20 h followed by ethionamide 2 mg/L for 4 h at 37°C without agitation.Nucleic Acid Extraction - The pellets were resuspended in 1 mL of RNAproTM (FastRNA Pro Blue Kit, MP biomedicals) and homogenized in impact-resistant 2 mL tubes containing 0.1 mm silica spheres (Lysing Matrix B, MP biomedicals) using a FastPrep FP120 cell disrupter (Thermo Fisher Scientific) at 6.0 Hz for 40 s. The ribolysed cells were centrifuged at 12,000 x g to remove cellular debris and RNA was purified following the manufacturer's instructions. Ribosomal RNA (rRNA) depletion was performed using QIAseq FastSelect –5S/16S/23S Kits; Qiagen).OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Raw RNA-seq reads were processed with Illumina quality control tools using default settings. Sequences shorter than 50 bp and/or that contained any ‘Ns’ and/or with a mean quality score lower than 30 were removed using PRINSEQ (http://prinseq.sourceforge.net/index.html). Next, rRNA-specific reads were filtered out by mapping all the reads on M. tuberculosis rRNA sequences using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Analysis of the RNA sequencing data was conducted using the SPARTA open-source software package with default parameters (https://sparta.readthedocs.io/en/latest/).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNAMycobacterium tuberculosisAlpibectir-Ethionamide (AlpE) as a novel drug combination for the treatment of tuberculosisZainab Edoo, Camille Grosse, Thomas Maitre, Rosangela Frita, Aurélie Chauffour, Laure Fournier Le Ray, Alexandre Godmer, Alexandra Aubry, Marilyne Bourotte, Rudy Antoine, Lina Tawk, Stéphanie Slupek, Vincent Trebosc, Birgit Schellhorn, Aurore Dreneau, Line Hofmann, Christian Kemmer, Sergio Lociuro, Glenn E. Dale, Françoise Jung, Esther Pérez-Herrán, Alfonso Mendoza, Maria Jose Rebollo López, Sonja Ghidelli-Disse, Thilo Werner, Lluis Ballell, David Barros Aguirre, Vanessa Mathys, Karine Soetaert, Véronique Megalizzi, René Wintjens, Marc Gitzinger, Benoit Deprez, Nicolas Veziris, Modesto J Remuiñán, Nicolas Willand, Michel Pieren, Alain R. BaulardAlain BaulardZainab EdooRudy AntoinefalseRNA-seq of Mycobacterium tuberculosis H37Rv treated with alpibectir or a combination of alpibectir and ethionamide against untreated controlsAlpibectir potentiates the activity of ethionamide and prothionamide, which are second-line antibiotics used for tuberculosis treatment. Both are prodrugs whose antibacterial activity depends on bioactivation by oxidases, including the Baeyer-Villiger monooxygenase MymA. Alpibectir binds the transcriptional regulator VirS, increasing MymA expression and potentiating Eto and Pto activity. To determine the transcriptional response of M. tuberculosis to alpibectir, we treated cultures at an optical density of 0.7 with alpibectir 0.1 mg/L for 24 h. Alternatively, we determined the transcriptional response of cultures first treated with alpibectir 0.1 mg/L for 20 h followed by ethionamide 2 mg/L for 4 h. Untreated controls (DMSO 0.1%) were included.2025-12-10T00:00:00Z2026-06-16T14:01:04.276Z2025-11-22T21:56:58.443ZE-MTAB-16253ERP185509EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003816EFO_0003738EFO_0003969EFO_0004184