Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms

Abstract

Overflow metabolism is well known for yeast, bacteria and mammalian cells. It typically occurs under glucose excess conditions and is characterized by excretions of by-products such as ethanol, acetate or lactate. This phenomenon, also denoted the short-term Crabtree effect, has been extensively studied over the past few decades, however, its basic regulatory mechanism and functional role in metabolism is still unknown. Here we present a comprehensive quantitative and time-dependent analysis of the exometabolome of Escherichia coli, Corynebacterium glutamicum, Bacillus licheniformis, and Saccharomyces cerevisiae during well-controlled bioreactor cultivations. Most surprisingly, in all cases a great diversity of central metabolic intermediates and amino acids is found in the culture medium with extracellular concentrations varying in the micromolar range. Different hypotheses for these observations are formulated and experimentally tested. As a result, the intermediates in the culture medium during batch growth must originate from passive or active transportation due to a new phenomenon termed “extended” overflow metabolism. Moreover, we provide broad evidence that this could be a common feature of all microorganism species when cultivated under conditions of carbon excess and non-inhibited carbon uptake. In turn, this finding has consequences for metabolite balancing and, particularly, for intracellular metabolite quantification and 13C-metabolic flux analysis.

Control of Clostridium difficile Physiopathology in Response to Cysteine Availability

“…In a broad range of bacteria, including E. coli and Bacillus licheniformis, pyruvate is excreted into the medium at the end of the exponential growth phase under the conditions of overflow metabolism. This compound is further taken up and metabolized (79,80). In E. coli, the two-component system (TCS) YpdA-YpdB, which is also present in B. licheniformis (81), reacts predominantly to the presence of exogenous pyruvate and induces the expression of yhjX, which encodes a transporter of the major facilitator superfamily (79).…”

Identification of a Target Gene and Activating Stimulus for the YpdA/YpdB Histidine Kinase/Response Regulator System in Escherichia coli

“…An increase in the extracellular pyruvate level occurs when the rate of production of pyruvate temporarily exceeds the bacterium's capacity to metabolize the compound (43). Under conditions of overflow metabolism, pyruvate, like acetate, is a major component of the exometabolome in a broad range of bacteria (44). Sugar acids, e.g., gluconate or glucuronate, are predominantly metabolized via the Entner-Doudoroff pathway in E. coli, resulting in the production of 2 pyruvates per sugar acid (45).…”

“…The carbonscavenging regulon includes cyclic AMP (cAMP)/cAMP receptor protein (CRP), which mediates the use of alternative carbon sources (47). Furthermore, previously excreted compounds (e.g., pyruvate) are rapidly taken up to drive continuing growth (44). The second response includes global reprogramming for starvation and the transition into the stationary phase (48).…”

Metabolomic Analysis of Schizosaccharomyces pombe: Sample Preparation, Detection, and Data Interpretation

“…One aspect that has not been deeply covered in microorganisms (Paczia et al 2012)-and remains virtually untouched in fission yeast-is that of the extracellular metabolome (exometabolome), including excretion of secondary metabolites (Krug and Muller 2014). Another interesting topic is the analysis of metabolic fluxes, also called fluxomics (Mo et al 2009;Celton et al 2012).…”