{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Zainab Edoo"],"organism":["Mycobacterium tuberculosis"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17255"],"description":["M. tuberculosis H37Rv cultures were exposed to BVL3572S in the absence or presence of L-histidine or L-alanine for at least 4 weeks. Individual colonies were picked and their genomic DNA extracted, indexed, and sequenced."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - 7 mL of exponentially growing cultures were harvested by centrifugation at 3,500 x g for 5 min.","Nucleic Acid Extraction - Pellets were resuspended in 500 µL of UltraPure™ Phenol:Chloroform:Isoamyl Alcohol (Thermo Fisher 15593031), 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. Samples were mixed with 500 µL TE buffer (10 mM Tris pH 8.5, 1 mM EDTA) and incubated for 5 min at room temperature before centrifugation (10 min, 10,000 rpm, 4 °C). The aqueous phase (400 µL) was transferred to a new tube, to which 80 µL sodium acetate (4 M, pH 5.5) and 800 µL of 100% cold ethanol were added. DNA was precipitated overnight at - 20 °C. After centrifugation (30 min, 12,000 rpm, 4 °C), the supernatant was removed, and the pellet was washed twice with 700 µL of 70% cold ethanol followed by centrifugation (15 min, 12,000 rpm, 4 °C). Pellets were air-dried for around 30 min and resuspended in 35 µL nuclease-free water. DNA was quantified by Qubit dsDNA BR assay kit (ThermoFisher Scientific).","Sequencing - Quantified libraries were pooled and sequenced on Illumina platforms according to the effective library concentration and required data amount. Sequencing kit: NovaSeq X Series 25B Reagent Kit (300 Cycle)- XLEAP-SBS chemistry","Library Construction - The genomic DNA was randomly sheared into short fragments. The obtained fragments were end repaired, A-tailed and further ligated with Illumina adapter. The resulting fragments with adapters were size-selected and PCR-amplified before proceeding for purification. The library was quantified through Qubit and qPCR, and size distribution detected with fragment analyzer. Library preparation kit: Novogene NGS DNA Library Prep Set (Cat No.PT004)","Growth Protocol - Plates containing Middlebrook 7H10 or 7H9 solid medium supplemented with glycerol 0.2%, Tween 80 0.05% and OADC 10% were prepared with BVL3572S alone (7H9) or in the presence of L-His 3 mM (7H9) or L-Ala 3 mM (7H10). 7H9 solid medium was used for mutant selection with L-His or alone because we suspected our 7H10 stock to contain trace amounts of L-Ala. Plates were inoculated with 106, 107, or 108 CFUs of a weeks-old culture of Mtb H37Rv (OD600 nm > 1) and incubated at 37 °C for at least 4 weeks. Individual colonies were picked and cultured until exponential phase in the presence of the corresponding amino acid if applicable."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Sequencing reads from WT and mutant strains were quality-filtered and aligned to the reference genome. Single-nucleotide variants and small insertions/deletions were identified by variant calling and filtered based on quality metrics. Variants present in the WT strain were excluded, and the remaining mutant-specific variants were annotated."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"pubmed_abstract":["Tuberculosis remains the leading cause of death from a single infectious agent worldwide, and the growing prevalence of multi-drug resistant  Mycobacterium tuberculosis (  Mtb ) underscores the urgent need for antibiotics with novel mechanisms of action. Here, we characterize BVL3572S, a hydroxamic acid-containing compound that is bactericidal and potently inhibits the growth of both extracellular and intracellular  Mtb . Integrated transcriptomic, genetic, and biochemical analyses identified the pyridoxal phosphate (PLP)-dependent aminotransferases HisC (Rv1600) and AlaA (Rv0337c; formerly AspC) as the primary molecular targets of BVL3572S, thereby simultaneously impacting L-histidine and L-alanine biosynthesis. Spontaneous resistance mutants harbored mutations in  hisC or  alaA . Target engagement was further supported by overexpression studies: AlaA overexpression increased resistance in the presence of L-His whereas HisC overexpression paradoxically increased susceptibility. X-ray crystallography revealed a covalent adduct between PLP and BVL3572S within the HisC active site. The short occupancy of this adduct suggests a futile cycle that sequesters PLP. Isotopic labeling revealed widespread perturbation of amino acid biosynthesis, consistent with PLP starvation. The stepwise resistance observed upon supplementation with L-His and L-Ala together or with PLP alone suggests inhibition of multiple targets. Genome-scale CRISPRi and Tn-seq analyses additionally indicated disruptions in central metabolism, cell envelope integrity, and redox balance, possibly due to PLP depletion cascades. Consistent with its inhibition of AlaA, BVL3572S displayed strong synergy with D-cycloserine, a second-line antitubercular drug targeting D-alanine synthesis and impacting peptidoglycan synthesis, highlighting the potential of this compound in combination therapy. Collectively, our findings establish BVL3572S as a promising lead compound acting through a previously unexploited, multitarget mechanism that induces broad metabolic stress in  Mtb , offering a novel therapeutic strategy against drug-resistant tuberculosis."],"study_type":["DNA-seq"],"species":["Mycobacterium tuberculosis"],"pubmed_title":["Exploiting Vitamin B6 Dependency: BVL3572S Inhibits HisC and AlaA to Kill Mycobacterium tuberculosis"],"pubmed_authors":["Zainab Edoo, Astrid Lenne-Delmotte, Camille Grosse, Marie Devaere, Marion Michel, Guillaume Caron, Ernesto Anoz-Carbonell, Kamel Djaout, Rosangela Frita, Cyril Gaudin, Line Hofmann, Sophie Lecher, Véronique Megalizzi, Alessia Michelotti, David Rengel, Pauline Rouan, Stephanie Slupek, Lina Tawk, Rudy Antoine, Hanna Kulyk, Glenn Dale, Christophe Guilhot, Nicolas Willand, Guy Lippens, René Wintjens, Alain Baulard","Alain Baulard","Cyril Gaudin","Zainab Edoo"],"additional_accession":[]},"is_claimable":false,"name":"Whole genome sequencing of spontaneous resistant mutants of Mycobacterium tuberculosis H37Rv selectec in the presence of BVL3572S and amino acids","description":"M. tuberculosis H37Rv cultures were exposed to BVL3572S in the absence or presence of L-histidine or L-alanine for at least 4 weeks. Individual colonies were picked and their genomic DNA extracted, indexed, and sequenced.","dates":{"release":"2026-06-03T00:00:00Z","modification":"2026-06-30T22:41:32.81Z","creation":"2026-06-30T22:41:17.261Z"},"accession":"E-MTAB-17255","cross_references":{"ENA":["ERP195937"],"Biostudies":["E-MTAB-16773"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002693","EFO_0005518","EFO_0003816","EFO_0004184"],"doi":["10.1101/2025.10.27.684782"]}}