Phosphoglycerate mutase knock‐out mutant Saccharomyces cerevisiae: Physiological investigation and transcriptome analysis

Abstract

The yeast Saccharomyces cerevisiae is able to adapt its metabolism to grow on different carbon sources and to shift to non‐fermentative growth on C2 or C3 carbon sources (ethanol, acetate, or glycerol) through the activation of gluconeogenesis. Here, we studied the response to the deletion of the glycolytic and gluconeogenic gene GPM1, encoding for phosphoglycerate mutase. It was previously shown that a S. cerevisiae strain with non‐functional copies of GPM1 can only grow when glycerol and ethanol are both present as carbon sources, whilst addition of glucose was shown to strongly inhibit growth. It was suggested that glycerol is needed to feed gluconeogenesis whilst ethanol is required for respiration. Here, we studied the physiological response of the GPM1 knock‐out mutant through fermentation and transcriptome analysis. Furthermore, we compared the physiological results with those obtained through simulations using a genome‐scale metabolic model, showing that glycerol is only needed in small amounts for growth. Our findings strongly suggest a severely impaired growth ability of the knock‐out mutant, which presents increased transcript levels of genes involved in the pentose phosphate pathway and in the glyoxylate shunt. These results indicate an attempt to compensate for the energy imbalance caused by the deletion of the glycolytic/gluconeogenic gene within the mutant.

Negative feedback of glycolysis and oxidative phosphorylation: Mechanisms of and reasons for it

“…1). We confirmed the data of Papini et al [38] and showed that, similar to glucose, galactose inhibits the growth of Δgpm1 cells (Fig. 2).…”

“…The Δgpm1 strain can grow in the presence of a mixture of glycerol and acetate (or ethanol) as carbon sources. In this case acetate (or ethanol) is metabolized downstream of phosphoglycerate mutase and produces substrates for the Krebs cycle, while glycerol is consumed by the enzymes upstream of phos phoglycerate mutase and serves as a substrate for gluco neogenesis [38]. It was shown that addition of glucose inhibits growth of Δgpm1 cells [39].…”

Triosephosphates as intermediates of the Crabtree effect

“…4). These data agree with the data of Papini and coworkers [24]. This work describes the effect of phosphoglycerate mutase dele tion on gene expression.…”

“…This work describes the effect of phosphoglycerate mutase dele tion on gene expression. In particular, they showed that the deletion stimulates the expression of many stress response genes [24]. Thus, the regulatory role of triosephosphates in yeast physiology requires further study.…”

Evolutionary significance of metabolic network properties

“…A checkmark indicates that the reaction catalysed by the enzyme has a significant centrality in the corresponding species; a hyphen indicates not significant; n.a. indicates the corresponding enzyme is not annotated for the species.enzymeEC no.BSECSCCRATHSreferencescatalase1.11.1.6✓✓✓—✓n.a.[34,35]superoxide dismutase1.15.1.1✓✓n.a.—✓✓[36–38]carbonic anhydrase4.2.1.1✓—✓✓✓n.a.[39–45] l -arabinose isomerase5.3.1.4✓✓n.a.n.a.n.a.✓[46,47]phosphoglycerate mutase5.4.2.1✓—✓——✓[48–51]…”