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Metabolomics for Secondary Metabolite Research
Article

Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae

1
Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
2
Agilent Technologies, Life Sciences, Diagnostics and Applied Markets, Santa Clara, CA 95051, USA
3
Biology Department, San Francisco State University, San Francisco, CA 94132, USA
*
Author to whom correspondence should be addressed.
Metabolites 2013, 3(4), 1102-1117; https://doi.org/10.3390/metabo3041102
Received: 15 October 2013 / Revised: 20 November 2013 / Accepted: 25 November 2013 / Published: 6 December 2013
(This article belongs to the Special Issue Microbial Metabolomics)
Previous studies have shown that calcium stressed Saccharomyces cerevisiae, challenged with immunosuppressant drugs FK506 and Cyclosporin A, responds with comprehensive gene expression changes and attenuation of the generalized calcium stress response. Here, we describe a global metabolomics workflow for investigating the utility of tracking corresponding phenotypic changes. This was achieved by efficiently analyzing relative abundance differences between intracellular metabolite pools from wild-type and calcium stressed cultures, with and without prior immunosuppressant drugs exposure. We used pathway database content from WikiPathways and YeastCyc to facilitate the projection of our metabolomics profiling results onto biological pathways. A key challenge was to increase the coverage of the detected metabolites. This was achieved by applying both reverse phase (RP) and aqueous normal phase (ANP) chromatographic separations, as well as electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) sources for detection in both ion polarities. Unsupervised principle component analysis (PCA) and ANOVA results revealed differentiation between wild-type controls, calcium stressed and immunosuppressant/calcium challenged cells. Untargeted data mining resulted in 247 differentially expressed, annotated metabolites, across at least one pair of conditions. A separate, targeted data mining strategy identified 187 differential, annotated metabolites. All annotated metabolites were subsequently mapped onto curated pathways from YeastCyc and WikiPathways for interactive pathway analysis and visualization. Dozens of pathways showed differential responses to stress conditions based on one or more matches to the list of annotated metabolites or to metabolites that had been identified further by MS/MS. The purine salvage, pantothenate and sulfur amino acid pathways were flagged as being enriched, which is consistent with previously published literature for transcriptomics analysis. Thus, broad discovery-based data mining combined with targeted pathway projections can be an important asset for rapidly distilling, testing and evaluating a large amount of information for further investigation. View Full-Text
Keywords: untargeted metabolomics; Saccharomyces cerevisiae; yeast; calcium; calcineurin; FK506; Cyclosporin A; stress response untargeted metabolomics; Saccharomyces cerevisiae; yeast; calcium; calcineurin; FK506; Cyclosporin A; stress response
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MDPI and ACS Style

Jenkins, S.; Fischer, S.M.; Chen, L.; Sana, T.R. Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae. Metabolites 2013, 3, 1102-1117. https://doi.org/10.3390/metabo3041102

AMA Style

Jenkins S, Fischer SM, Chen L, Sana TR. Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae. Metabolites. 2013; 3(4):1102-1117. https://doi.org/10.3390/metabo3041102

Chicago/Turabian Style

Jenkins, Stefan, Steven M. Fischer, Lily Chen, and Theodore R. Sana 2013. "Global LC/MS Metabolomics Profiling of Calcium Stressed and Immunosuppressant Drug Treated Saccharomyces cerevisiae" Metabolites 3, no. 4: 1102-1117. https://doi.org/10.3390/metabo3041102

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