Proteome dynamics during transition from exponential to stationary phase in yeast

Glycolysis is the central pathway for sugar metabolism in most living organisms. The single celled eukaryote yeast is a widely used model organism for higher eukaryotes in which the regulation of glycolysis is widely studied. S. cerevisiae is one of the few eukaryotic organisms that can efficiently grow under both aerobic and anaerobic conditions. Furthermore, this yeast switches from proliferation into a resting phase when nutrients are exhausted. However, little is known about the proteome dynamics that takes place during this transition, particularly under anaerobic conditions. Moreover, like many other organisms including humans, the genome of S. cerevisiae contains duplications which result in the expression of so called ‘isoenzymes’ in central metabolic pathways including glycolysis. Interestingly, the role of those ‘isoenzymes’ remains elusive to date. Here we describe a large-scale quantitative proteome study combining shotgun experiments using a nano-LC coupled to a QE plus Orbitrap mass spectrometer (Thermo, Germany), to capture the proteome dynamics during transition from proliferation into stationary phase, under both aerobic and anaerobic growth. Furthermore, we explore the proteome dynamics of a mutant yeast where the glycolytic isoenzymes are deleted.