Conservation of the metabolomic response to starvation across two divergent microbes.
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 alpha-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.
Brauer
Matthew J
MJ
Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA.
Yuan
Jie
J
Bennett
Bryson D
BD
Lu
Wenyun
W
Kimball
Elizabeth
E
Botstein
David
D
Rabinowitz
Joshua D
JD
D002244:Carbon / Q000172:deficiency*; D002853:Chromatography, Liquid; D016000:Cluster Analysis; D004734:Energy Metabolism / Q000502:physiology*; D048168:Escherichia coli K12 / Q000378:metabolism / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D013058:Mass Spectrometry; D009584:Nitrogen / Q000172:deficiency*; D010667:Phenylpyruvic Acids / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000378:metabolism / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D013045:Species Specificity
D029968:Escherichia coli Proteins; D010667:Phenylpyruvic Acids; D029701:Saccharomyces cerevisiae Proteins; D002244:Carbon; D009584:Nitrogen; C031606:phenylpyruvic acid