Isolation of two cell populations from yeast during high-level alcoholic fermentation that resemble quiescent and nonquiescent cells from the stationary phase on glucose

The characteristics of differentiated yeast subpopulations depend on their lifestyle and available nutrients

Yeast populations can undergo diversification during their growth and ageing, leading to the formation of different cell-types. Differentiation into two major subpopulations, differing in cell size and density and exhibiting distinct physiological and metabolic properties, was described in planktonic liquid cultures and in populations of colonies growing on semisolid surfaces. Here, we compare stress resistance, metabolism and expression of marker genes in seven differentiated cell subpopulations emerging during cultivation in liquid fermentative or respiratory media and during colony development on the same type of solid media. The results show that the more-dense cell subpopulations are more stress resistant than the less-dense subpopulations under all cultivation conditions tested. On the other hand, respiratory capacity, enzymatic activities and marker gene expression differed more between subpopulations. These characteristics are more influenced by the lifestyle of the population (colony vs. planktonic cultivation) and the medium composition. Only in the population growing in liquid respiratory medium, two subpopulations do not form as in the other conditions tested, but all cells exhibit a range of characteristics of the more-dense subpopulations. This suggests that signals for cell differentiation may be triggered by prior metabolic reprogramming or by an unknown signal from the structured environment in the colony.

A Systematic Review on Quiescent State Research Approaches in S. cerevisiae

Quiescence, the temporary and reversible arrest of cell growth, is a fundamental biological process. However, the lack of standardization in terms of reporting the experimental details of quiescent cells and populations can cause confusion and hinder knowledge transfer. We employ the systematic review methodology to comprehensively analyze the diversity of approaches used to study the quiescent state, focusing on all published research addressing the budding yeast Saccharomyces cerevisiae. We group research articles into those that consider all cells comprising the stationary-phase (SP) population as quiescent and those that recognize heterogeneity within the SP by distinguishing phenotypically distinct subpopulations. Furthermore, we investigate the chronological age of the quiescent populations under study and the methods used to induce the quiescent state, such as gradual starvation or abrupt environmental change. We also assess whether the strains used in research are prototrophic or auxotrophic. By combining the above features, we identify 48 possible experimental setups that can be used to study quiescence, which can be misleading when drawing general conclusions. We therefore summarize our review by proposing guidelines and recommendations pertaining to the information included in research articles. We believe that more rigorous reporting on the features of quiescent populations will facilitate knowledge transfer within and between disciplines, thereby stimulating valuable scientific discussion.

Renewing Lost Genetic Variability with a Classical Yeast Genetics Approach

Due to their long domestication time course, many industrial Saccharomyces cerevisiae strains are adopted in numerous processes mostly for historical reasons instead of scientific and technological needs. As such, there is still significant room for improvement for industrial yeast strains relying on yeast biodiversity. This paper strives to regenerate biodiversity with the innovative application of classic genetic methods to already available yeast strains. Extensive sporulation was indeed applied to three different yeast strains, specifically selected for their different origins as well as backgrounds, with the aim of clarifying how new variability was generated. A novel and easy method to obtain mono-spore colonies was specifically developed, and, to reveal the extent of the generated variability, no selection after sporulation was introduced. The obtained progenies were then tested for their growth in defined mediums with high stressor levels. A considerable and strain-specific increase in both phenotypic and metabolomic variability was assessed, and a few mono-spore colonies were found to be of great interest for their future exploitation in selected industrial processes.

Role of Dead Cells in Collective Stress Tolerance in Microbial Communities: Evidence from Yeast

A substantial part of yeast life cycle takes place in the communities where the cells are surrounded by their own clones. Meanwhile, yeast cell fitness depends not only on its own adaptations but also on the processes in the neighboring cells. Moreover, even if a cell loses its clonogenic ability, it is still capable of protecting surrounding cells that are still alive. Dead cells can absorb lipophilic antibiotics and provide nutrients to their kin neighbors. Some enzymes can be released into the environment and detoxify exogenous toxins. For example, cytosolic catalase, which degrades hydrogen peroxide, can stay active outside of the cell. Inviable cells of pathogenic yeast species can suppress host immune responses and, in this way, boost spread of the pathogen. In this review, we speculate that biochemical processes in dying cells can facilitate increase of stress resistance in the alive kin cells and therefore be a subject of natural selection. We considered possible scenarios of how dead microbial cells can increase survival of their kin using unicellular fungi - baker's yeast Saccharomyces cerevisiae - as an example. We conclude that the evolutionary conserved mechanisms of programmed cell death in yeast are likely to include a module of early permeabilization of the cell plasma membrane rather than preserve its integrity.

Trehalose Mediated Inhibition of Lactate Dehydrogenase from Rabbit Muscle. The Application of Kramers' Theory in Enzyme Catalysis

Lactate dehydrogenase (LDH) catalyzes the reduction of pyruvate to lactate by using NADH. LDH kinetics has been proposed to be dependent on the dynamics of a loop over the active site. Kramers' theory has been useful in the study of enzyme catalysis dependent on large structural dynamics. In this work, LDH kinetics was studied in the presence of trehalose and at different temperatures. In the absence of trehalose, temperature increase raised exponentially the LDH V_max and revealed a sigmoid transition of K_m toward a low-affinity state similar to protein unfolding. Notably, LDH V_max diminished when in the presence of trehalose, while pyruvate affinity increased and the temperature-mediated binding site transition was hindered. The effect of trehalose on k_cat was viscosity dependent as described by Kramers' theory since V_max correlated inversely with the viscosity of the medium. As a result, activation energy ( E_a) for pyruvate reduction was dramatically increased by trehalose presence. This work provides experimental evidence that the dynamics of a structural component in LDH is essential for catalysis, i.e., the closing of the loop on the active site. While the trehalose mediated-increased of pyruvate affinity is proposed to be due to the compaction and/or increase of structural order at the binding site.

Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives

Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.

Effect of aerobic and microaerophilic culture in the growth dynamics of Saccharomyces cerevisiae and in training of quiescent and non-quiescent subpopulations

Saccharomyces cerevisiae is industrially the most important yeast, and its growth in different concentrations of oxygen can be used to improve various application processes. The aims of this work were to study in aerobic and microaerophilic growth conditions the cell size and tendency of morphological changes in S. cerevisiae in different stages of growth and to assess the effect of the two growth conditions in the differentiation of quiescent and non-quiescent subpopulations in the stationary phase. Dissolved oxygen levels in the culture medium for aerobic and microaerophilic conditions were 6.6 and 5.2 mg L(-1), respectively. In both growth conditions, similar viable cell populations were obtained, although in aerobic conditions the stationary phase was reached and the quiescent and non-quiescent subpopulations were also differentiated. The microaerophilic growth produced a significant reduction in the specific growth rate and consequently also in glucose and oxygen consumption. The most notable changes in cellular size and morphology occurred with the depletion of glucose and oxygen. The concentration of dissolved oxygen in the culture medium significantly modulated the growth kinetics of S. cerevisiae and their development and differentiation to quiescent cells. This could justify the need to readjust small variations in oxygen levels during yeast cultures in biotechnological processes.

Uncoupling reproduction from metabolism extends chronological lifespan in yeast

Studies of replicative and chronological lifespan in Saccharomyces cerevisiae have advanced understanding of longevity in all eukaryotes. Chronological lifespan in this species is defined as the age-dependent viability of nondividing cells. To date this parameter has only been estimated under calorie restriction, mimicked by starvation. Because postmitotic cells in higher eukaryotes often do not starve, we developed a model yeast system to study cells as they age in the absence of calorie restriction. Yeast cells were encapsulated in a matrix consisting of calcium alginate to form ∼3 mm beads that were packed into bioreactors and fed ad libitum. Under these conditions cells ceased to divide, became heat shock and zymolyase resistant, yet retained high fermentative capacity. Over the course of 17 d, immobilized yeast cells maintained >95% viability, whereas the viability of starving, freely suspended (planktonic) cells decreased to <10%. Immobilized cells exhibited a stable pattern of gene expression that differed markedly from growing or starving planktonic cells, highly expressing genes in glycolysis, cell wall remodeling, and stress resistance, but decreasing transcription of genes in the tricarboxylic acid cycle, and genes that regulate the cell cycle, including master cyclins CDC28 and CLN1. Stress resistance transcription factor MSN4 and its upstream effector RIM15 are conspicuously up-regulated in the immobilized state, and an immobilized rim15 knockout strain fails to exhibit the long-lived, growth-arrested phenotype, suggesting that altered regulation of the Rim15-mediated nutrient-sensing pathway plays an important role in extending yeast chronological lifespan under calorie-unrestricted conditions.

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

Unprecedented proteome plasticity in response to stress in yeast is revealed using a novel screening platform that allows tracking of protein localization and abundance at single-cell resolution.

Uncovering the mechanisms underlying robust responses of cells to stress is crucial for our understanding of cellular physiology. Indeed, vast amounts of data have been collected on transcriptional responses in Saccharomyces cerevisiae. However, only a handful of pioneering studies describe the dynamics of proteins in response to external stimuli, despite the fact that regulation of protein levels and localization is an essential part of such responses. Here we characterized unprecedented proteome plasticity by systematically tracking the localization and abundance of 5,330 yeast proteins at single-cell resolution under three different stress conditions (DTT, H₂O₂, and nitrogen starvation) using the GFP-tagged yeast library. We uncovered a unique “fingerprint” of changes for each stress and elucidated a new response arsenal for adapting to radical environments. These include bet-hedging strategies, organelle rearrangement, and redistribution of protein localizations. All data are available for download through our online database, LOQATE (localization and quantitation atlas of yeast proteome).

A loss-of-function mutation in the PAS kinase Rim15p is related to defective quiescence entry and high fermentation rates of Saccharomyces cerevisiae sake yeast strains

Sake yeast cells have defective entry into the quiescent state, allowing them to sustain high fermentation rates. To reveal the underlying mechanism, we investigated the PAS kinase Rim15p, which orchestrates initiation of the quiescence program in Saccharomyces cerevisiae. We found that Rim15p is truncated at the carboxyl terminus in modern sake yeast strains as a result of a frameshift mutation. Introduction of this mutation or deletion of the full-length RIM15 gene in a laboratory strain led to a defective stress response, decreased synthesis of the storage carbohydrates trehalose and glycogen, and impaired G(1) arrest, which together closely resemble the characteristic phenotypes of sake yeast. Notably, expression of a functional RIM15 gene in a modern sake strain suppressed all of these phenotypes, demonstrating that dysfunction of Rim15p prevents sake yeast cells from entering quiescence. Moreover, loss of Rim15p or its downstream targets Igo1p and Igo2p remarkably improved the fermentation rate in a laboratory strain. This finding verified that Rim15p-mediated entry into quiescence plays pivotal roles in the inhibition of ethanol fermentation. Taken together, our results suggest that the loss-of-function mutation in the RIM15 gene may be the key genetic determinant of the increased ethanol production rates in modern sake yeast strains.

Ethanol fermentation driven by elevated expression of the G1 cyclin gene CLN3 in sake yeast

Cellular and subcellular morphology reflects the physiological state of a cell. To determine the physiological nature of sake yeast with superior fermentation properties, we quantitatively analyzed the morphology of sake yeast cells by using the CalMorph system. All the sake strains examined here exhibited common morphological traits that are typically observed in the well-characterized whiskey (whi) mutants that show accelerated G(1)/S transition. In agreement with this finding, the sake strain showed less efficient G(0)/G(1) arrest and elevated expression of the G(1) cyclin gene CLN3 throughout the fermentation period. Furthermore, deletion of CLN3 remarkably impaired the fermentation rate in both sake and laboratory strains. Disruption of the SWI6 gene, a transcriptional coactivator responsible for Cln3p-mediated G(1)/S transition, also resulted in a decreased fermentation rate, whereas whi mutants exhibited significant improvement in the fermentation rate, demonstrating positive roles of Cln3p and its downstream signalling pathway in facilitating ethanol fermentation. The combined results indicate that enhanced induction of CLN3 contributes to the high fermentation rate of sake yeast, which are natural whi mutants.

Proliferation/quiescence: the controversial "aller-retour"

The vast majority of cells, from prokaryotes up to vertebrate organisms, spend most of their time in quiescence, a state defined as a temporary and reversible absence of proliferation. Establishing the quiescent state while maintaining the capacity to re-enter the proliferation cycle are critical for cell survival and must be tightly orchestrated to avoid pathological proliferation. Hence, studying the biology of quiescent cells is an exciting research field. Taking advantage of technical progress in genomic, transcriptomic and metabolomic, the nature of transitions between proliferation and quiescence have been recently re-visited in budding yeast. Together with new findings in cell biology, these studies resuscitate an old demon in the field: the controversial existence of a "quiescence program".

Influence of cell parameters in Fourier transform infrared spectroscopy analysis of whole yeast cells

Fourier Transform InfraRed spectroscopy (FTIR) is an emerging technique in biology. One of the analytical problems inherent with this approach is the extreme variability typical of biological systems. Extrinsic fonts of variations are the growth media and the growth phase of the microbial culture. In order to gain knowledge on the relations between these two factors and the spectral variability, metabolomic changes in Saccharomyces cerevisiae cells during growth were analyzed with FTIR spectroscopy. Spectral variations reflected the changes occurring in all cellular compartments and components during the different growth stages and describe the metabolomic evolution of cell cultures during growth. Three different media were tested. Different mathematical and statistical treatments were used to describe and evaluate the changes occurring during growth. Variations were mainly concentrated in the exponential phase, whereas fewer changes occurred in stationary phase cells. The three different media caused different metabolomic behaviours during growth. The mathematical distance between the peak areas of amide I, amide II and of two distinct peaks in the carbohydrates region could give a synthetic description of growth and produced similar trends in all the conditions tested. The distance between the two carbohydrate peaks could be used to determine the mid exponential phase and the entrance in the stationary phase. Growth phase was shown to influence the sensitivity of a FTIR-based cell stress bioassay. The knowledge of the metabolomic variations during growth could be used in the future to optimize FTIR applications in microbiology.

Sake yeast strains have difficulty in entering a quiescent state after cell growth cessation

Sake yeast strains produce a high concentration of ethanol during sake brewing compared to laboratory yeast strains. As ethanol fermentation by yeast cells continues even after cell growth stops, analysis of the physiological state of the stationary phase cells is very important for understanding the mechanism of producing higher concentrations of ethanol. We compared the physiological characteristics of stationary phase cells of both sake and laboratory yeast strains in an aerobic batch culture and under sake brewing conditions. We unexpectedly found that sake yeast cells in the stationary phase had a lower buoyant density and stress tolerance than did the laboratory yeast cells under both experimental conditions. These results suggest that it is difficult for sake yeast cells to enter a quiescent state after cell growth has stopped, which may be one reason for the higher fermentation rate of sake yeast compared to laboratory yeast strains.

The proteomics of quiescent and nonquiescent cell differentiation in yeast stationary-phase cultures

As yeast cultures enter stationary phase in rich, glucose-based medium, differentiation of two major subpopulations of cells, termed quiescent and nonquiescent, is observed. Differences in mRNA abundance between exponentially growing and stationary-phase cultures and quiescent and nonquiescent cells are known, but little was known about protein abundance in these cells. To measure protein abundance in exponential and stationary-phase cultures, the yeast GFP-fusion library (4159 strains) was examined during exponential and stationary phases, using high-throughput flow cytometry (HyperCyt). Approximately 5% of proteins in the library showed twofold or greater changes in median fluorescence intensity (abundance) between the two conditions. We examined 38 strains exhibiting two distinct fluorescence-intensity peaks in stationary phase and determined that the two fluorescence peaks distinguished quiescent and nonquiescent cells, the two major subpopulations of cells in stationary-phase cultures. GFP-fusion proteins in this group were more abundant in quiescent cells, and half were involved in mitochondrial function, consistent with the sixfold increase in respiration observed in quiescent cells and the relative absence of Cit1p:GFP in nonquiescent cells. Finally, examination of quiescent cell-specific GFP-fusion proteins revealed symmetry in protein accumulation in dividing quiescent and nonquiescent cells after glucose exhaustion, leading to a new model for the differentiation of these cells.