Metabolomics in systems microbiology

Abstract

Because of the importance of microbes as model organisms, biotechnology tools, and contributors to mammalian and ecosystem metabolism, there has been longstanding interest in measuring their metabolite levels. Current metabolomic methods, involving mass spectrometry-based measurement of cell extracts, enable routine quantitation of most central metabolites. Metabolomics alone, however, is inadequate to understand cellular metabolic activity: Flux measurement and proteomic, genetic, and biochemical approaches with a metabolomics bent are all needed. Here we highlight examples where these integrated methods have contributed to discovery of metabolic pathways, regulatory interactions, and homeostasis mechanisms. We also indicate enduring challenges concerning unstable and low abundance compounds, subcellular compartmentalization, and quantitative amalgamation of different data types.

Figure 1. Overview of metabolomics in systems microbiology

Metabolomic and genomics provide complementary information for identifying an organism’s metabolic capabilities. Concentration data for metabolites, proteins, and transcripts can be used for regulatory inference. Computational integration of such data aims to enable the development of mechanistically accurate, predictive metabolic models.

Figure 2. Elucidation of the methanol assimilation pathway in Methylobacterium extorquens AM1

Metabolomics identified the intermediates of the novel ethylmalonyl-CoA pathway for methanol assimilation. Isotopic tracing from ¹³C-acetate confirmed the reaction sequence. Small graphs on the right side of the figure show percent ¹³C-labeling versus time.

Figure 3. Metabolome dynamics reveal a role for purine salvage in the yeast respiro-fermentative transition

Using isotopic standards and LC-MS to quantitate purine salvage pathway intermediates, Walther et al. solved the long-standing mystery of counter-intuitive total adenosine phosphate (AXP) depletion following glucose addition to respiring yeast. AXP is shuttled through IMP and inosine to prevent AMP accumulation and associated impairment of growth by low adenylate energy charge.