Dynamic Metabolic Footprinting Reveals the Key Components of Metabolic Network in Yeast Saccharomyces cerevisiae

Pramote Chumnanpuen, Michael Adsetts Edberg Hansen, Jørn Smedsgaard, Jens Nielsen

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Abstract

Metabolic footprinting offers a relatively easy approach to exploit the potentials of metabolomics for phenotypic characterization of microbial cells. To capture the highly dynamic nature of metabolites, we propose the use of dynamic metabolic footprinting instead of the traditional method which relies on analysis at a single time point. Using direct infusion-mass spectrometry (DI-MS), we could observe the dynamic metabolic footprinting in yeast S. cerevisiae BY4709 (wild type) cultured on 3 different C-sources (glucose, glycerol, and ethanol) and sampled along 10 time points with 5 biological replicates. In order to analyze the dynamic mass spectrometry data, we developed the novel analysis methods that allow us to perform correlation analysis to identify metabolites that significantly correlate over time during growth on the different carbon sources. Both positive and negative electrospray ionization (ESI) modes were performed to obtain the complete information about the metabolite content. Using sparse principal component analysis (Sparse PCA), we further identified those pairs of metabolites that significantly contribute to the separation. From the list of significant metabolite pairs, we reconstructed an interaction map that provides information of how different metabolic pathways have correlated patterns during growth on the different carbon sources.
Original languageEnglish
Article number894296
JournalInternational Journal of Plant Genomics
Number of pages14
ISSN2314-436x
DOIs
Publication statusPublished - 2014

Bibliographical note

This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Keywords

  • metabolomic
  • Fungi Plantae (Fungi, Microorganisms, Nonvascular Plants, Plants) - Ascomycetes [15100] Saccharomyces cerevisiae species strain-BY4709
  • carbon 7440-44-0
  • ethanol 64-17-5
  • glucose 58367-01-4
  • glycerol 56-81-5
  • 10060, Biochemistry studies - General
  • 10068, Biochemistry studies - Carbohydrates
  • 13002, Metabolism - General metabolism and metabolic pathways
  • 51519, Plant physiology - Metabolism
  • direct infusion-mass spectrometry laboratory techniques, spectrum analysis techniques
  • dynamic metabolic footprinting laboratory techniques
  • electrospray ionization laboratory techniques, spectrum analysis techniques
  • phenotypic characterization laboratory techniques, genetic techniques
  • sparse principal component analysis mathematical and computer techniques
  • Metabolism
  • Methods and Techniques

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