Metabolic-rate dependent cell cycle entry and progression in Saccharomyces cerevisiae

De celdelingscyclus - het proces waarbij twee dochtercellen worden gevormd uit één oorspronkelijke moedercel - is essentieel voor voortzetting van het leven, en fouten in de regulatie van dit proces kunnen leiden tot ziektes. Aangezien celdeling een energetisch en biosynthetisch zeer kostbaar proces is, moeten cellen nauwkeurig beslissen wanneer ze het programma van celdeling uitvoeren. Recente bevindingen toonden aan dat enkele fenotypische aspecten van microbiële cellen bepaald kunnen worden door metabole snelheden, oftewel fluxen, onafhankelijk van de extracellulaire beschikbaarheid van voedingsstoffen. Deze bevindingen inspireerden de hypothese dat de beslissing van knopvormende gist om het celdelingsproces uit te voeren afhankelijk is van metabole fluxen. Gebruikmakend van methoden op zowel enkel cel- als populatieniveau, werd gevonden dat de snelheid van de glycolyse inderdaad kan bepalen of gistcellen het celdelingsproces doorlopen, onafhankelijk van de extracellulaire beschikbaarheid van glucose. Bovendien werd gevonden dat, naast de invloed op het wel of niet plaatsvinden van celdeling, de activiteit van de stofwisseling ook belangrijk is voor de uitvoering van dit proces. Meer specifiek werd er gevonden dat, hoewel DNA replicatie grotendeels ongevoelig is voor de snelheid van de glycolyse, de ongehinderde vorming van een dochtercel een voldoende hoge flux door de glycolyse vereist. Ten slotte, in de zoektocht naar een mechanistisch verband tussen metabole snelheden en controle over de celcyclus, werd er gevonden dat de zeer dynamische snelheid van de eiwitsynthese een piek vertoont vlak voordat toewijding aan de celdelingscyclus plaatsvindt, wat leidt tot een toename in de concentratie van een belangrijke activator van de celcyclus

Metabolic-flux dependent regulation of microbial physiology

According to the most prevalent notion, changes in cellular physiology primarily occur in response to altered environmental conditions. Yet, recent studies have shown that changes in metabolic fluxes can also trigger phenotypic changes even when environmental conditions are unchanged. This suggests that cells have mechanisms in place to assess the magnitude of metabolic fluxes, that is, the rate of metabolic reactions, and use this information to regulate their physiology. In this review, we describe recent evidence for metabolic flux-sensing and flux-dependent regulation. Furthermore, we discuss how such sensing and regulation can be mechanistically achieved and present a set of new candidates for flux-signaling metabolites. Similar to metabolic-flux sensing, we argue that cells can also sense protein translation flux. Finally, we elaborate on the advantages that flux-based regulation can confer to cells

Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

A comprehensive description of the phenotypic changes during cellular aging is key towards unraveling its causal forces. Previously, we mapped age-related changes in the proteome and transcriptome (Janssens et al., 2015). Here, employing the same experimental procedure and model-based inference, we generate a comprehensive account of metabolic changes during the replicative life of Saccharomyces cerevisiae. With age, we found decreasing metabolite levels, decreasing growth and substrate uptake rates accompanied by a switch from aerobic fermentation to respiration, with glycerol and acetate production. The identified metabolic fluxes revealed an increase in redox cofactor turnover, likely to combat increased production of reactive oxygen species. The metabolic changes are possibly a result of the age-associated decrease in surface area per cell volume. With metabolism being an important factor of the cellular phenotype, this work complements our recent mapping of the transcriptomic and proteomic changes towards a holistic description of the cellular phenotype during aging

Yeast Ataxin-2 Forms an Intracellular Condensate Required for the Inhibition of TORC1 Signaling during Respiratory Growth

Yeast ataxin-2, also known as Pbp1 (polyA binding protein-binding protein 1), is an intrinsically disordered protein implicated in stress granule formation, RNA biology, and neurodegenerative disease. To understand the endogenous function of this protein, we identify Pbp1 as a dedicated regulator of TORC1 signaling and autophagy under conditions that require mitochondrial respiration. Pbp1 binds to TORC1 specifically during respiratory growth, but utilizes an additional methionine-rich, low complexity (LC) region to inhibit TORC1. This LC region causes phase separation, forms reversible fibrils, and enables self-association into assemblies required for TORC1 inhibition. Mutants that weaken phase separation in vitro exhibit reduced capacity to inhibit TORC1 and induce autophagy. Loss of Pbp1 leads to mitochondrial dysfunction and reduced fitness during nutritional stress. Thus, Pbp1 forms a condensate in response to respiratory status to regulate TORC1 signaling

Calorie restriction does not elicit a robust extension of replicative lifespan in Saccharomyces cerevisiae

Calorie restriction (CR) is often described as the most robust manner to extend lifespan in a large variety of organisms. Hence, considerable research effort is directed toward understanding the mechanisms underlying CR, especially in the yeast Saccharomyces cerevisiae. However, the effect of CR on lifespan has never been systematically reviewed in this organism. Here, we performed a meta-analysis of replicative lifespan (RLS) data published in more than 40 different papers. Our analysis revealed that there is significant variation in the reported RLS data, which appears to be mainly due to the low number of cells analyzed per experiment. Furthermore, we found that the RLS measured at 2% (wt/vol) glucose in CR experiments is partly biased toward shorter lifespans compared with identical lifespan measurements from other studies. Excluding the 2% (wt/vol) glucose experiments from CR experiments, we determined that the average RLS of the yeast strains BY4741 and BY4742 is 25.9 buds at 2% (wt/vol) glucose and 30.2 buds under CR conditions. RLS measurements with a microfluidic dissection platform produced identical RLS data at 2% (wt/vol) glucose. However, CR conditions did not induce lifespan extension. As we excluded obvious methodological differences, such as temperature and medium, as causes, we conclude that subtle method-specific factors are crucial to induce lifespan extension under CR conditions in S. cerevisiae

Saccharomyces cerevisiae goes through distinct metabolic phases during its replicative lifespan

A comprehensive description of the phenotypic changes during cellular aging is key towards unraveling its causal forces. Previously, we mapped age-related changes in the proteome and transcriptome (Janssens et al., 2015). Here, employing the same experimental procedure and model-based inference, we generate a comprehensive account of metabolic changes during the replicative life of Saccharomyces cerevisiae. With age, we found decreasing metabolite levels, decreasing growth and substrate uptake rates accompanied by a switch from aerobic fermentation to respiration, with glycerol and acetate production. The identified metabolic fluxes revealed an increase in redox cofactor turnover, likely to combat increased production of reactive oxygen species. The metabolic changes are possibly a result of the age-associated decrease in surface area per cell volume. With metabolism being an important factor of the cellular phenotype, this work complements our recent mapping of the transcriptomic and proteomic changes towards a holistic description of the cellular phenotype during aging.status: publishe