Modelling of glucose repression signalling in yeast Saccharomyces cerevisiae

Abstract

Saccharomyces cerevisiae has a sophisticated signalling system that plays a crucial role in cellular adaptation to changing environments. The SNF1 pathway regulates energy homeostasis upon glucose derepression, hence, plays an important role in various processes, such as metabolism, cell cycle, autophagy. To unravel its behaviour, SNF1 signalling has been extensively studied. However, the pathway components are strongly interconnected and inconstant; therefore, elucidating its dynamic behaviour based on experimental data only is challenging. To tackle this complexity, systems biology approaches have been successfully employed. This review summarises the progress, advantages and disadvantages of the available mathematical modelling frameworks covering Boolean, dynamic kinetic, single-cell models, which have been used to study processes and phenomena ranging from crosstalks to sources of cell-to-cell variability in the context of SNF1 signalling. Based on the lessons from existing models, we further discuss how to develop a consensus dynamic mechanistic model of the entire SNF1 pathway that can provide novel insights into the dynamics of nutrient signalling.

Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing

“…Hitherto, many mathematical models describing protein damage accumulation (reviewed in [23,24]), signalling pathways (reviewed in [25,26]) and metabolism [27] have been developed. Flux balance analysis (FBA) models have been extensively applied to predict fluxes through genome-scale reconstructions of metabolic networks of many different organisms and conditions [27][28][29][30].…”

Sir2 and Glycerol Underlie the Pro-Longevity Effect of Quercetin during Yeast Chronological Aging

“…Hence, QUER brings about trehalose accumulation at the expense of the main compatible solute/osmolyte glycerol, albeit CR-restricted chronological aging cells face an extreme survival-based metabolism. Both trehalose and glycerol are compatible solutes, the accumulation and interplay of which have been shown to occur in yeast during various stress conditions to maximize the probability of cell survival and/or proliferation [53][54][55]. However, trehalose has more specific roles in protecting proteins and preserving membrane structures, along with being the carbohydrate of choice for surviving starvation and upon cell cycle reentry from starvation [20,43].…”

Multi-scale model suggests the trade-off between protein and ATP demand as a driver of metabolic changes during yeast replicative ageing

“…Hitherto, many mathematical models describing protein damage accumulation (reviewed in [25,26]), signalling pathways (reviewed in [27,28]) and metabolism [29] have been developed. Flux balance analysis (FBA) models have been extensively applied to predict fluxes through genome-scale reconstructions of metabolic networks of many different organisms and conditions [29][30][31][32].…”