Can we predict the intracellular metabolic state of a cell based on extracellular metabolite data?

Abstract

The analysis of extracellular metabolites presents many technical advantages over the analysis of intracellular compounds, which made this approach very popular in recent years as a high-throughput tool to assess the metabolic state of microbial cells. However, very little effort has been made to determine the actual relationship between intracellular and extracellular metabolite levels. The secretion of intracellular metabolites has been traditionally interpreted as a consequence of an intracellular metabolic overflow, which is based on the premise that for a metabolite to be secreted, it must be over-produced inside the cell. Therefore, we expect to find a secreted metabolite at increased levels inside the cells. Here we present a time-series metabolomics study of Saccharomyces cerevisiae growing on a glucose-limited chemostat with parallel measurements of intra- and extracellular metabolites. Although most of the extracellular metabolites were also detected in the intracellular samples and showed a typical metabolic overflow behaviour, we demonstrate that the secretion of many metabolites could not be explained by the metabolic overflow theory.

Microbial metabolomics: essential definitions and the importance of cultivation conditions for utilizing Bacillus species as bionematicides

“…Results indicated that the intracellular and extracellular levels of aspartate, 2‐oxoglutarate, benzoate and decanoate changed in opposite directions, while a total of six metabolites were uniquely detected in the spent culture media (Granucci et al . ).…”

“…; Granucci et al . ). The supernatant obtained is then used for the metabolomics analysis (Pinu et al .…”

“…The metabolic overflow theory states that intracellular intermediates of metabolic pathways can be secreted extracellularly when these intermediates accumulate within the cell (Granucci et al . ) due to imbalanced intracellular metabolic pathways (Pinu et al . ).…”

“…According to Granucci et al . (), the analysis of extracellular metabolites is technically advantageous over that of intracellular metabolites most likely due to their accessibility and ease of handling (Villas‐Bôas et al . ).…”

“…When compared to intracellular metabolites, extracellular metabolites have lower turnover rates due to the dilution, low abundance or complete absence of enzymes outside the cell (Pinu et al 2017). According to Granucci et al (2015), the analysis of extracellular metabolites is technically advantageous over that of intracellular metabolites most likely due to their accessibility and ease of handling (Villas-Bôas et al 2007). When the focus of a study is on the extracellular metabolites, the metabolites are quantified in the supernatant when the microbial cells are separated from the cultivation media (Pinu et al 2017) by means of filtration or centrifugation (Mashego et al 2007;Granucci et al 2015).…”