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PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database
Weiliang Huang1, Luke K Brewer1, Jace W Jones1
1Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21209, USA.
Nucleic Acids Research
|November 7, 2017
Summary
The Pseudomonas aeruginosa Metabolome Database (PAMDB) offers a comprehensive resource for studying this pathogen
Area of Science:
- Microbiology and Bioinformatics
- Metabolomics
- Systems Biology
Background:
- Pseudomonas aeruginosa is an opportunistic pathogen with versatile metabolism, crucial for biofilm formation, quorum sensing, and bioremediation.
- Understanding its metabolic pathways is key to developing new diagnostics and therapeutics.
- Existing metabolome databases lack specific, detailed information for P. aeruginosa.
Purpose of the Study:
- To develop and present the Pseudomonas aeruginosa Metabolome Database (PAMDB).
- To provide a searchable, annotated resource for P. aeruginosa metabolites and pathways.
- To facilitate research in P. aeruginosa biology, pathology, and potential applications.
Main Methods:
- Compilation of data from electronic databases, literature, and laboratory mass spectrometry (MS) metabolomic data.
- Integration of metabolite information including chemical structures, physiochemical properties, and spectral data (NMR, MS).
- Linking metabolites to genes, proteins, and metabolic pathways, modeled after existing databases like ECMDB, YMDB, and HMDB.
Main Results:
- PAMDB contains over 4370 metabolites and 938 pathways.
- Database includes links to over 1260 genes and proteins.
- Provides detailed compound information, including spectra, enzymes, and pathway associations.
Conclusions:
- PAMDB is a valuable, searchable resource for P. aeruginosa research.
- The database supports the identification of active compounds, biomarkers, and diagnostic tools.
- Future iterations will enhance its utility for biologists, chemists, and clinicians.
