Standards of sugar phosphates were purchased from Sigma-Aldrich: α-D-fructose-6-phosphate (F1502-1G), α-D-glucose-6-phosphate (G7250), α-D-glucose-1-phosphate (G7000-5G), calbiochem α-D-mannose-6-phosphate (444100-50MG) and Biosynth Ltd for β-D-glucose-1-phosphate (MG02984). The metabolites in the samples were identified based on their m/z values and retention times compared to those of the standards.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - hilic"],"chromatography_protocol":["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 x 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":["Rv3400 is a phosphoglucomutase required for trehalose metabolism in Mycobacterium tuberculosis."],"submitter_name":["Yi Liu"],"submitter_affiliation":["Imperial College London"],"organism_part":["Chemical","Intracellular"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Bacterial pellets were washed once with cold sterile PBS and metabolically quenched in extraction solution (40% acetonitrile, 40% methanol, 20% ddH2O). Samples were transferred to microtubes containing 0.1 mm acid-washed zirconia beads and lysed using a FastPrep-24 homogeniser twice at 6.0 m/s for 30 seconds, with a 5-minute interval. Supernatants were transferred to 0.22 μm spin X column filters (Costar) and filtered twice by centrifuging at 15,000 x g for 30 minutes. After filtration, the flowthrough was mixed with equal volume of acetonitrile and centrifuged at 15,000 x g for 10 minutes. 100 µL of mixture was loaded into polypropylene snap vials (Agilent Technologies) for LC-MS analysis.
"],"organism":["Chemical","Mycobacterium tuberculosis"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS13438"],"author":["Yi Liu. Imperial College London. Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom. yi.liu13@imperial.ac.uk.","Gerald Larrouy-Maumus. Imperial College London. Centre for Bacterial Resistance Biology, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom. g.larrouy-maumus@imperial.ac.uk."],"data_transformation_protocol":["MassHunter Qualitative Analysis software was used to check the extracted ion chromatograms of the m/z values of interest and obtain their retention times, which were used to construct the personal compound database and library (PCDL) for following analysis. MassHunter Profinder B8.0 was used to extract the stable isotope labelling patterns from PCDL.
"],"study_factor":["Treatment","Genotype","Concentration","Dilution factor","Technical replicate","Biological replicate"],"submitter_email":["yi.liu13@imperial.ac.uk"],"sample_collection_protocol":["Mtb strains were grown in 10 mL flasks with 7H9 medium to reach an OD600nm of approximately 0.8. After incubation, bacteria were collected by centrifugation at 3,000 × g and 4 °C for 10 minutes.
"],"omics_type":["Metabolomics"],"study_design":["Liquid Chromatography","Metabolomics","Mycobacterium tuberculosis","Trehalose","targeted metabolites"],"curator_keywords":["Liquid Chromatography","Metabolomics","Mycobacterium tuberculosis","Trehalose","targeted metabolites"],"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":["Fructose 6-phosphate","Ergothioneine","Mycothiol","Glucose 6-phosphate","Mannose phosphate","β-D-glucose-1-phosphate","α-D-glucose-1-phosphate","Mycothione"],"additional_accession":[]},"is_claimable":false,"name":"Rv3400 is a phosphoglucomutase required for trehalose metabolism in Mycobacterium tuberculosis","description":"Mycobacterium tuberculosis is a global killer causing over a million deaths from tuberculosis (TB) every year. It is therefore a major burden on human health. To reduce the deadly impact of TB, we need a better understanding of the strategies used by M. tuberculosis to adapt its metabolism to survive and persist in the human host. This will help us design better strategies for TB treatment and control. Previous enzymological studies have reported that the Mtb rv3400 gene encodes a β-phosphoglucomutase; however, its role in M. tuberculosis metabolism has not been investigated. In the present study, we show that deletion of rv3400 leads to a 30-fold increase in β-D-glucose 1-phosphate, confirming its primary function as a β-phosphoglucomutase. Additionally, deletion of rv3400 leads to a growth defect when trehalose is the sole carbon source, indicating that this enzyme is required for optimal use of trehalose, an essential disaccharide in mycobacteria.
","dates":{"publication":"2026-08-07","submission":"2025-12-02"},"accession":"MTBLS13438","cross_references":{"MetaboLights":["MTBLC 14314","MTBLC 88003","MTBLC 616988","MTBLC 16218","MTBLC 29042","MTBLC 16768","MTBLC 16086","MTBLC 4828"],"ChEBI":["CHEBI: 14314","CHEBI: 88003","CHEBI: 616988","CHEBI: 16218","CHEBI: 29042","CHEBI: 16768","CHEBI: 16086","CHEBI: 4828"]}}