Conservation of the metabolomic response to starvation across two divergent microbes

Matthew J. Brauer, Jie Yuan, Bryson D. Bennett, Wenyun Lu, Elizabeth Kimball, David Botstein, Joshua D. Rabinowitz

Research output: Contribution to journalArticlepeer-review

222 Scopus citations


We followed 68 cellular metabolites after carbon or nitrogen starvation of Escherichia coli and Saccharomyces cerevisiae, using a filter-culture methodology that allows exponential growth, nondisruptive nutrient removal, and fast quenching of metabolism. Dynamic concentration changes were measured by liquid chromatography-tandem mass spectrometry and viewed in clustered heat-map format. The major metabolic responses anticipated from metabolite-specific experiments in the literature were observed as well as a number of novel responses. When the data were analyzed by singular value decomposition, two dominant characteristic vectors were found, one corresponding to a generic starvation response and another to a nutrient-specific starvation response that is similar in both organisms. Together these captured a remarkable 72% of the metabolite concentration changes in the full data set. The responses described by the generic starvation response vector (42%) included, for example, depletion of most biosynthetic intermediates. The nutrient-specific vector (30%) included key responses such as increased phosphoenolpyruvate signaling glucose deprivation and increased α-ketoglutarate signaling ammonia deprivation. Metabolic similarity across organisms extends from the covalent reaction network of metabolism to include many elements of metabolome response to nutrient deprivation as well.

Original languageEnglish (US)
Pages (from-to)19302-19307
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number51
StatePublished - Dec 19 2006

All Science Journal Classification (ASJC) codes

  • General


  • Escherichia coli
  • Metabolomics
  • Nitrogen/carbon metabolism
  • Saccharomyces cerevisiae
  • Starvation response


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