Computational protocol: Amino Acid Catabolism in Staphylococcus aureus and the Function of Carbon Catabolite Repression

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Protocol publication

[…] The collected supernatants were lyophilized and reconstructed in NMR buffer (KH2PO4/K2HPO4 buffer–D2O [pH 7.4] [uncorrected], with 500 μM trimethylsilylpropanoic acid [TMSP] as an internal standard). Two-dimensional (2D) 1H-13C heteronuclear single-quantum coherence (HSQC) spectra were collected on a Bruker DRX Avance 500-MHz spectrometer equipped with a 5-mm-long triple-resonance cryoprobe (1H, 13C, and 15N) with a z axis gradient, a BACS-120 sample changer, Bruker IconNMR, and an automatic tuning and matching (ATM) unit. NMRPipe () and NMRViewJ () were used to process and analyze the collected spectra. The TMSP internal standard was used for chemical shift referencing and normalization of NMR peak intensities. NMR peaks from the 2D 1H-13C HSQC spectra were annotated by comparing the observed 1H and 13C chemical shifts to the metabolite reference data from the Platform for RIKEN metabolomics (PRIMe; http://prime.psc.riken.jp/) (), Human Metabolome Database (HMDB; http://www.hmdb.ca/) (), Madison metabolomics Consortium Database (http://mmcd.nmrfam.wisc.edu/) (), Metabominer (http://wishart.biology.ualberta.ca/metabominer/) (), and BiomagResBank (BMRB; http://www.bmrb.wisc.edu//) () with error tolerances of 0.08 ppm and 0.25 ppm for 1H and 13C chemical shifts, respectively. The relative intensity (i.e., concentration) of each metabolite was calculated by averaging the intensities of all NMR peaks unambiguously assigned to the metabolite. […]

Pipeline specifications

Software tools NMRViewJ, MetaboMiner
Databases HMDB BMRB MMCD PRIMe
Application NMR-based metabolomics
Organisms Staphylococcus aureus, Epipremnum aureum
Diseases Infection, Soft Tissue Infections
Chemicals Adenosine Triphosphate, Amino Acids, Carbon, Glucose, Nitrogen, Oxygen, Glutamic Acid, Pyruvic Acid, Oxaloacetic Acid