Metabolite identification was based on mass-retention times and isotope distribution patterns.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["The data were acquired with an Agilent 1290 Infinity II UHPLC coupled to a 6545 LC/Q-TOF system. Chromatographic separation was performed with an Agilent InfinityLab Poroshell 120 HILIC-Z (2.1 × 100 mm, 2.7 μm (p/n 675775-924)) column. The HILIC-Z methodology was optimized for polar acidic metabolites. Column compartment was set at 50°C. For easy and consistent mobile-phase preparation, a concentrated 10 × solution consisting of 100 mM ammonium acetate (pH 9.0) in water was prepared to produce mobile phases A and B. Mobile phase A consisted of 10 mM ammonium acetate in water (pH 9) with a 5 μM Agilent InfinityLab deactivator additive (p/n 5191-4506), and mobile phase B consisted of 10 mM ammonium acetate (pH 9) in 10:90 (v:v) water/acetonitrile with a 5 μM Agilent InfinityLab deactivator additive (p/n 5191-4506). The following gradient was applied at a flow rate of 0.25 ml/min: 0 min, 96% B; 2 min, 96% B; 5.5 min, 88% B; 8.5 min, 88% B; 9 min, 86% B; 14 min, 86% B; 17 min, 82% B; 23 min, 65% B; 24 min, 65% B; 24.5 min, 96% B; 26 min, 96% B and 3-min of re-equilibration at 96% B.
"],"publication":["Mycobacterium tuberculosis VadK required for regulation of the methylcitrate cycle and virulence."],"submitter_name":["Jordan Pascoe"],"submitter_affiliation":["University of Oxford"],"organism_part":["endometabolome"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["The bacteria were metabolically quenched by plunging into acetonitrile/methanol/H2O (2:2:1) precooled to -80 °C. Metabolites were extracted by bead beating in the FastPrep at 6.5 for 20 s with careful cooling in between. Soluble extracts were filtered twice through 0.22 μm Spin-X column filters (CoStar) and then stored at −80°C until analysis.
"],"organism":["Mycobacterium tuberculosis"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS13906"],"author":["Jordan Pascoe. University of Oxford. jordan.pascoe@biology.ox.ac.uk.","Dany Beste. University of Surrey. d.beste@surrey.ac.uk."],"data_transformation_protocol":["Data analysis was performed using the Agilent MassHunter Qualitative (v10), Quantitative Analysis and Profinder Softwares. Metabolites were quantified and the area under the curve (AUC) was determined. AUC was normalized to protein concentration determined using a standard Bradford assay.
"],"study_factor":["13C isotopomer"],"submitter_email":["jordan.pascoe@biology.ox.ac.uk"],"sample_collection_protocol":["Mtb strains were grown in standard 7H9 media to late log phase (OD=0.8-1) before being washed and resuspended in 13C labelled media and incubated for 48 h. Using [U-13C3]-glycerol (99%), 20 mM [U-13C3]-pyruvate (99%) or 0.154% [3, 4-13C2] cholesterol for 48hrs.
"],"omics_type":["Metabolomics"],"study_design":["13C","Metabolomics","Mycobacterium tuberculosis","metabolic flux","Isotope Labeling","6545 Q-TOF LC/MS"],"curator_keywords":["Metabolomics","13C","Mycobacterium tuberculosis","metabolic flux","Isotope Labeling","6545 Q-TOF LC/MS"],"mass_spectrometry_protocol":["Accurate MS was performed using an Agilent Accurate Mass 6545 QTOF apparatus. Dynamic mass axis calibration was achieved by continuous infusion after the chromatography of a reference mass solution using an isocratic pump connected to an electrospray ionization source operated in negative-ion mode. The following parameters were used: gas temperature, 225°C; drying gas, 13 l min-1; sheath gas temperature, 350 °C; nebulizer pressure, 35 psi; sheath gas flow, 12 l min-1; capillary voltage, 3,500 V; nozzle voltage, 0 V; fragmentor voltage, 125 V; skimmer 45V and octupole 1 RF voltage, 750V. The data were collected in centroid 4 GHz (extended dynamic range) mode.
"],"metabolite_name":["Tyrosine","Methylisocitrate","Alanine","Succinate","Serine","Pyruvate","Glutamate","Glycine","Histidine","Malate","Fructose-6-Phosphate","Valine","Isocitrate","Gamma-aminobutyric acid","aspartic acid"],"additional_accession":[]},"is_claimable":false,"name":"Mycobacterium tuberculosis VadK required for regulation of the methylcitrate cycle and virulence","description":"The evolution of new enzymatic functions is constrained and guided by the architecture of an organism’s metabolic and regulatory networks and environmental constraints. Here, we identify a kinase that has evolved from pyruvate phosphate dikinase. Through biochemical and systems-level analyses, we show that this enzyme, encoded by Rv1127c in Mycobacterium tuberculosis (Mtb), has diverged from its ancestral role in central carbon metabolism to function as a histidine kinase in pathogenic mycobacteria and related species. We designate this enzyme Virulence Associated DiKinase (VadK), reflecting its ability to autophosphorylate and role in virulence. VadK is essential for the utilization of carbon sources critical for survival within the host and to cause tuberculosis in murine models. Furthermore, VadK interacts with enzymes of the methylcitrate cycle, and 13C-tracer experiments demonstrates that it fine-tunes flux through this pathway, with elevated flux proving growth limiting. Together, these findings identify VadK as a regulatory kinase that integrates metabolic control with virulence in Mtb, revealing a new facet of metabolic regulation in bacterial pathogenesis and a potential target for therapeutic intervention.
","dates":{"publication":"2026-04-21","submission":"2026-02-15"},"accession":"MTBLS13906","cross_references":{"MetaboLights":["MTBLC57305","MTBLC17822","MTBLC15595","MTBLC15607","MTBLC30031","MTBLC16865","MTBLC22660","MTBLC32484","MTBLC36453","MTBLC16449","MTBLC18186","MTBLC16084","MTBLC27570","MTBLC32861","MTBLC15361"],"ChEBI":["CHEBI:57305","CHEBI:17822","CHEBI:15595","CHEBI:15607","CHEBI:30031","CHEBI:16865","CHEBI:22660","CHEBI:32484","CHEBI:36453","CHEBI:16449","CHEBI:18186","CHEBI:16084","CHEBI:27570","CHEBI:32861","CHEBI:15361"]}}