Differential scaling between G1 protein production and cell size dynamics promotes commitment to the cell division cycle in budding yeast.

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.

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.

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 methodspecific factors are crucial to induce lifespan extension under CR conditions in S. cerevisiae.I n the last decades, a nutritious diet low in calories, commonly referred to as calorie restriction (CR), has been reported to extend the lifespan of a broad range of organisms, such as yeast, worms, fruit flies, mice, rats, and monkeys (1-6). This seemingly evolutionary conserved effect of CR on aging has sparked intense investigation into its underlying molecular mechanisms, especially in the budding yeast Saccharomyces cerevisiae (7-10). Some studies suggest that nutrient-responsive pathways, such as target of rapamycin (TOR), protein kinase A (PKA), and Sch9 (11), mediate CR-induced lifespan extension, whereas others hypothesize that CR increases the activity of sirtuin deacetylases (e.g., SIR2) extending lifespan by suppressing ribosomal DNA recombination (9, 12, 13).In S. cerevisiae, lifespan can either be defined by the time cells remain viable in absence of nutrients, called chronological lifespan, or by the number of daughter cells a yeast cell produces during its life, which is referred to as replicative lifespan (RLS) (14). Although RLS can vary greatly between individual yeast cells, the average RLS (i.e., across a population of cells) is assumed to be a genotypic trait (15-19). However, besides CR, other environmental conditions, such as pH and carbon source, are known to have a strong impact on RLS (20, 21).Here, through a systematic analysis of RLS data of S. cerevisiae using data from more than 27,000 cells, we obtained indication that small sample sizes might be the cause for the often observed significant variation between RLS data. Further, we identified that partly biased data exis...

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.