Abstract
BackgroundA well known example of oscillatory phenomena is the transient oscillations of glycolytic intermediates in Saccharomyces cerevisiae, their regulation being predominantly investigated by mathematical modeling. To our knowledge there has not been a genetic approach to elucidate the regulatory role of the different enzymes of the glycolytic pathway.ResultsWe report that the laboratory strain BY4743 could also be used to investigate this oscillatory phenomenon, which traditionally has been studied using S. cerevisiae X2180. This has enabled us to employ existing isogenic deletion mutants and dissect the roles of isoforms, or subunits of key glycolytic enzymes in glycolytic oscillations. We demonstrate that deletion of TDH3 but not TDH2 and TDH1 (encoding glyceraldehyde-3-phosphate dehydrogenase: GAPDH) abolishes NADH oscillations. While deletion of each of the hexokinase (HK) encoding genes (HXK1 and HXK2) leads to oscillations that are longer lasting with lower amplitude, the effect of HXK2 deletion on the duration of the oscillations is stronger than that of HXK1. Most importantly our results show that the presence of beta (Pfk2) but not that of alpha subunits (Pfk1) of the hetero-octameric enzyme phosphofructokinase (PFK) is necessary to achieve these oscillations. Furthermore, we report that the cAMP-mediated PKA pathway (via some of its components responsible for feedback down-regulation) modulates the activity of glycoytic enzymes thus affecting oscillations. Deletion of both PDE2 (encoding a high affinity cAMP-phosphodiesterase) and IRA2 (encoding a GTPase activating protein- Ras-GAP, responsible for inactivating Ras-GTP) abolished glycolytic oscillations.ConclusionsThe genetic approach to characterising the glycolytic oscillations in yeast has demonstrated differential roles of the two types of subunits of PFK, and the isoforms of GAPDH and HK. Furthermore, it has shown that PDE2 and IRA2, encoding components of the cAMP pathway responsible for negative feedback regulation of PKA, are required for glycolytic oscillations, suggesting an enticing link between these cAMP pathway components and the glycolysis pathway enzymes shown to have the greatest role in glycolytic oscillation. This study suggests that a systematic genetic approach combined with mathematical modelling can advance the study of oscillatory phenomena.
Highlights
A well known example of oscillatory phenomena is the transient oscillations of glycolytic intermediates in Saccharomyces cerevisiae, their regulation being predominantly investigated by mathematical modeling
Glycolytic oscillations in S. cerevisiae BY4743 are comparable to those in X2180 Until this study, yeast glycolytic oscillations have been investigated in S. cerevisiae X2180, a strain rarely used in genetic analysis
We demonstrate for the first time that glycolytic oscillations could be observed in the standard reference genetic background strain BY4743
Summary
A well known example of oscillatory phenomena is the transient oscillations of glycolytic intermediates in Saccharomyces cerevisiae, their regulation being predominantly investigated by mathematical modeling. When glucosestarved Saccharomyces cerevisiae cells are incubated with glucose in the presence of the respiration inhibitor cyanide, transient oscillations of levels of relevant glycolytic metabolites can occur. These include levels of nicotinamide adenine dinucleotide (NAD) which can be seen to oscillate between the oxidized (NAD+) and reduced forms (NADH), as well as other glycolytic intermediates, including glucose-6-phosphate, fructose-6-phosphate and fructose 1,6-bisphosphate [1]. Glycolytic oscillations are an example of oscillatory phenomena, with others including waves of cAMP in Dictyostelium [8], circadian rhythms [9], oscillations of Ca2+ levels [10] and the cell cycle [11]
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