Temporal proteome dynamics of (minimal glycolysis) yeast during aerobic and anaerobic growth

Activity: Talk or presentationTalk or presentation at a conference

Description

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 broadly studied. S. cerevisiae is one of the few eukaryotic organisms that can efficiently grow under both aerobic and anaerobic conditions. This yeast switches from proliferation into a resting phase
when nutrients are exhausted. However, little is known about the proteome dynamics that take 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 socalled ‘isoenzymes’ in central metabolic pathways including glycolysis. Interestingly, the role of those
‘isoenzymes’ remains elusive to date. Here, we describe a large-scale quantitative shotgun proteome study using a nano-LC coupled to a QE plus Orbitrap mass spectrometer, 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 minimal glycolysis mutant yeast where the
glycolytic isoenzymes are deleted. TMT quantification of the identified yeast proteins was enabled by PEAKS Q and an open source data processing pipeline was developed in Python to streamline processing
and visualization of the large time-series experiments. The majority of essential pathways profoundly changed between aerobic and anaerobic conditions. For example, abundance differences were observed
in proteins involved in storage metabolism and stress response. Nevertheless, anaerobic growth showed substantially less re-organization during the transition from exponential to stationary phase. This supports
the conception that ‘anaerobic cells’ lack the time and resources to adapt to the changing environment. Notable, aerobic and anaerobic cultures undergo different trajectories into stationary phase, as aerobic
cells enter a ‘post-diauxic phase’ after glucose depletion, while anaerobic cells are not able to respire and enter stationary phase directly. However, the overall protein abundance of glycolytic proteins was
significantly higher in the anaerobically cultured cells in all growth phases, suggesting that cells compensate for the decreased ATP yield of strictly fermentative growth (anaerobic) versus respiratory
growth (aerobic), by increasing the glycolytic flux. On the other hand, while no phenotypic responses were observed when deleting the isoenzymes (previously), a range of protein-level alterations in
glycolysis were observed in the mutant, in particular under anaerobic conditions. For example, Tdh3 (Glyceraldehyde-3-phosphate dehydrogenase) was more abundant in the minimal glycolysis mutant than
in the wild-type yeast in the absence of oxygen. These subtle protein-level changes possibly compensate for the loss of the minor isoforms and thereby evading a stronger phenotype. The established proteome
data constitute an important step towards understanding the dynamic proteome organisation during nutrient exhaustion.
Period14 Jul 2022
Event titleInternational Specialised Symposium on Yeasts : Yeast Sea to Sky - Yeast in the Genomics Era
Event typeConference
Conference number36
LocationVancouver, Canada, British Columbia