Chronological lifespan of stationary phase yeast cells; a model for investigating the factors that might influence the ageing of postmitotic tissues in higher organisms

The histone deacetylase Hos2 forms an Hsp42-dependent cytoplasmic granule in quiescent yeast cells

One of many physiological adjustments in quiescent cells is spatial regulation of specific proteins and RNA important for the entry to or exit from the stationary phase. By examining the localization of epigenetic-related proteins in Saccharomyces cerevisiae, we observed the formation of a reversible cytosolic "stationary-phase granule" (SPG) by Hos2, a nuclear histone deacetylase. In the stationary phase, hos2 mutants display reduced viability. Additionally, they exhibit a significant delay when recovering from stationary phase. Hos2 SPGs also contained Hst2, a Sir2 homologue, and several stress-related proteins, including Set3, Yca1, Hsp26, Hsp42, and some known components of stress granules. However, Hos2 SPG formation does not depend on the formation of stress granules or processing bodies. The absence or presence of glucose is sufficient to trigger assembly or disassembly of Hos2 SPGs. Among the identified components of Hos2 SPGs, Hsp42 is the first and last member observed in the Hos2 SPG assembly and disassembly processes. Hsp42 is also vital for the relocalization of the other components to Hos2 SPGs, suggesting that Hsp42 plays a central role in spatial regulation of proteins in quiescent cells.

Maximising the yeast chronological lifespan

When investigating aging it is important to focus on the factors that are needed to attain, and which can be manipulated to extend, the longest lifespans. This has long been appreciated by those workers who use Drosophila or Caenorhabditis elegans as model experimental systems to study aging. Often though it seems it is not a consideration in many studies of yeast chronological aging. In this chapter I summarise how recent work has revealed the preconditioning that is needed for yeast to survive for long periods in stationary phase, therefore for it to exhibit a long chronological life span (CLS). Of critical importance in this regard is the nature of the nutrient limitation that, during the earlier growth phase, had forced the cells to undergo growth arrest. I have attempted to highlight those studies that have focussed on the longest CLSs, as this helps to identify investigations that may be addressing - not just factors that can influence chronological longevity - but those factors that are correlated with the authentic processes of chronological aging. Attempting to maximize long-term stationary survival in yeast should also enhance the potential relevance of this organism as an aging model to those who wrestle with the problems of aging in more complex systems. Finally I also give a personal perspective of how studies on the yeast CLS may still yet provide some important new insights into events that are correlated with aging.

Respiratory and TCA cycle activities affect S. cerevisiae lifespan, response to caloric restriction and mtDNA stability

We studied the importance of respiratory fitness in S. cerevisiae lifespan, response to caloric restriction (CR) and mtDNA stability. Mutants harboring mtDNA instability and electron transport defects do not respond to CR, while tricarboxylic acid cycle mutants presented extended lifespans due to CR. Interestingly, mtDNA is unstable in cells lacking dihydrolipoyl dehydrogenase under CR conditions, and cells lacking aconitase under standard conditions (both enzymes are components of the TCA and mitochondrial nucleoid). Altogether, our data indicate that respiratory integrity is required for lifespan extension by CR and that mtDNA stability is regulated by nucleoid proteins in a glucose-sensitive manner.

Apoptosis at inflection point in liquid culture of budding yeasts

Budding yeasts are highly suitable for aging studies, because the number of bud scars (stage) proportionally correlates with age. Its maximum stages are known to reach at 20–30 stages on an isolated agar medium. However, their stage dynamics in a liquid culture is virtually unknown. We investigate the population dynamics by counting scars in each cell. Here one cell division produces one new cell and one bud scar. This simple rule leads to a conservation law: “The total number of bud scars is equal to the total number of cells.” We find a large discrepancy: extremely fewer cells with over 5 scars than expected. Almost all cells with 6 or more scars disappear within a short period of time in the late log phase (corresponds to the inflection point). This discrepancy is confirmed directly by the microscopic observations of broken cells. This finding implies apoptosis in older cells (6 scars or more).

A genetic analysis of nitric oxide-mediated signaling during chronological aging in the yeast

In mammals, NO^•, a signaling molecule is implicated in the regulation of vasodilation, neurotransmission and immune response. It is believed that NO^• is a signaling molecule also in unicellular organism like yeast and may be involved in the regulation of apoptosis and sporulation. It has been reported that NO^• is produced during chronological aging (CA) leading to an increase of the superoxide level, which in turn mediates apoptosis. Since this conclusion was based on indirect measurements of NO^• by the Griess reaction, the role of NO^• signaling during CA in the yeast remains uncertain. We investigated this issue more precisely using different genetic and biochemical methodologies. We used cells lacking the factors influencing nitrosative stress response like flavohemoglobin metabolizing NO^•, S-nitrosoglutathione reductase metabolizing S-nitrosoglutathione and the transcription factor Fzf1p mediating NO^• response. We measured the standard parameters describing CA and found an elevation in the superoxide level, percentage of death cells, the level of TUNEL positive cells and a decrease in proliferating potential. These observations showed no significant differences between wild type cells and the disruptants except for a small elevation of the superoxide level in the Δsfa1 mutant. The intracellular NO^• level and flavohemoglobin expression decreased rather than increased during CA. Products of general nitrogen metabolism and protein tyrosine nitration were slightly decreased during CA, the magnitude of changes showing no differences between the wild type and the mutant yeast. Altogether, our data indicate that apoptosis during yeast CA is mediated by superoxide signaling rather than NO^• signaling.

Genetic approaches to aging in budding and fission yeasts: new connections and new opportunities

Yeasts are powerful model systems to examine the evolutionarily conserved aspects of eukaryotic aging because they maintain many of the same core cellular signaling pathways and essential organelles as human cells. We constructed a strain of the budding yeast Saccharomyces cerevisiae that could monitor the distribution of proteins involved in heterochromatic silencing and aging, and isolated mutants that alter this distribution. The largest class of such mutants cause defects in mitochondrial function, and appear to cause changes in nuclear silencing separate from the well-known Rtg2p-dependent pathway that alters nuclear transcription in response to the loss of the mitochondrial genome. Mutants that inactivate the ATP2 gene, which encodes the ATPase subunit of the mitochondrial F(1)F(0)-ATPase, were isolated twice in our screen and identify a lifespan extending pathway in a gene that is conserved in both prokaryotes and eukaryotes. The budding yeast S. cerevisiae S. cerevisiae has been used with great success to identify other lifespan-extending pathways in screens using surrogate phenotypes such as stress resistance or silencing to identify random mutants, or in high throughput screens that utilize the deletion strain set resource. However, the direct selection of long-lived mutants from a pool of random mutants is more challenging. We have established a new chronological aging assay for the evolutionarily distant fission yeast Schizosaccharomyces pombe that recapitulates aspects of aging conserved in all eukaryotes. We have constructed a novel S. pombe S. pombe DNA insertion mutant bank, and used it to show that we can directly select for a long-lived mutant. The use of both the budding and fission yeast systems should continue to facilitate the identification and validation of lifespan extending pathways that are conserved in humans.

Identification of evolutionarily conserved genetic regulators of cellular aging

To identify new genetic regulators of cellular aging and senescence, we performed genome-wide comparative RNA profiling with selected human cellular model systems, reflecting replicative senescence, stress-induced premature senescence, and distinct other forms of cellular aging. Gene expression profiles were measured, analyzed, and entered into a newly generated database referred to as the GiSAO database. Bioinformatic analysis revealed a set of new candidate genes, conserved across the majority of the cellular aging models, which were so far not associated with cellular aging, and highlighted several new pathways that potentially play a role in cellular aging. Several candidate genes obtained through this analysis have been confirmed by functional experiments, thereby validating the experimental approach. The effect of genetic deletion on chronological lifespan in yeast was assessed for 93 genes where (i) functional homologues were found in the yeast genome and (ii) the deletion strain was viable. We identified several genes whose deletion led to significant changes of chronological lifespan in yeast, featuring both lifespan shortening and lifespan extension. In conclusion, an unbiased screen across species uncovered several so far unrecognized molecular pathways for cellular aging that are conserved in evolution.

Differences in stationary-phase cells of a commercial Saccharomyces cerevisiae wine yeast grown in aerobic and microaerophilic batch cultures assessed by electric particle analysis, light diffraction and flow cytometry

We applied electric particle analysis, light diffraction and flow cytometry to obtain information on the morphological changes during the stationary phase of Saccharomyces cerevisiae. The reported analyses of S. cerevisiae populations were obtained under two different conditions, aerobic and microaerophilic, at 27°C. The samples analysed were taken at between 20 and 50 h from the beginning of culture. To assist in the interpretation of the observed distributions a complexity index was used. The aerobically grown culture reached significantly greater cell density. Under these conditions, the cell density experienced a much lower reduction (3%) compared with the microaerophilic conditions (30%). Under aerobic conditions, the mean cell size determined by both electric particle analysis and light diffraction was lower and remained similar throughout the experiment. Under microaerophilic conditions, the mean cell size determined by electric particle analysis decreased slightly as the culture progressed through the stationary phase. Forward and side scatter distributions revealed two cell subpopulations under both growth conditions. However, in the aerobic growing culture the two subpopulations were more separated and hence easier to distinguish. The distributions obtained with the three experimental techniques were analysed using the complexity index. This analysis suggested that a complexity index is a good descriptor of the changes that take place in a yeast population in the stationary phase, and that it aids in the discussion and understanding of the implications of these distributions obtained by these experimental techniques.

Surviving in the cold: yeast mutants with extended hibernating lifespan are oxidant sensitive

Metabolic activity generates oxidizing molecules throughout life, but it is still debated if the resulting damage of macromolecules is a causality, or consequence, of the aging process. This problem demands for studying growth- and longevity phenotypes separately. Here, we assayed a complete collection of haploid Saccharomyces cerevisiae knock-out strains for their capacity to endure long periods at low metabolic rates. Deletion of 93 genes, predominantly factors of primary metabolism, allowed yeast to survive for more than 58 months in the cold. The majority of these deletion strains were not resistant against oxidants or reductants, but many were hypersensitive. Hence, survival at low metabolic rates has limiting genetic components, and correlates with stress resistance inversely. Indeed, maintaining the energy consuming anti-oxidative machinery seems to be disadvantageous under coldroom conditions.

Calorie restriction reduces rDNA recombination independently of rDNA silencing

Calorie restriction (CR) extends lifespan in yeast, worms, flies and mammals, suggesting that it acts via a conserved mechanism. In yeast, activation of the NAD-dependent histone deacetylase, Sir2, by CR is thought to increase silencing at the ribosomal DNA, thereby reducing the recombination-induced generation of extrachromosomal rDNA circles, hence increasing replicative lifespan. Although accumulation of extrachromosomal rDNA circles is specific to yeast aging, it is thought that Sirtuin activation represents a conserved longevity mechanism through which the beneficial effects of CR are mediated in various species. We show here that growing yeast on 0.05 or 0.5% glucose (severe and moderate CR, respectively) does not increase silencing at either sub-telomeric or rDNA loci compared with standard (2% glucose) media. Furthermore, rDNA silencing was unaffected in the hxk2Δ, sch9Δ and tor1Δ genetic mimics of CR, but inhibited by FOB1 deletion. All these interventions extend lifespan in multiple yeast backgrounds, revealing a poor correlation between rDNA silencing and longevity. In contrast, CR and deletion of the FOB1, HXK2, SCH9 and TOR1 genes, all significantly reduced rDNA recombination. This silencing-independent mechanism for suppressing rDNA recombination may therefore contribute to CR-mediated lifespan extension.

A new Schizosaccharomyces pombe chronological lifespan assay reveals that caloric restriction promotes efficient cell cycle exit and extends longevity

We describe a new chronological lifespan (CLS) assay for the yeast Schizosaccharomyces pombe. Yeast CLS assays monitor the loss of cell viability in a culture over time, and this new assay shows a continuous decline in viability without detectable regrowth until all cells in the culture are dead. Thus, the survival curve is not altered by the generation of mutants that can grow during the experiments, and one can monitor the entire lifespan of a strain until the number of viable cells has decreased over 10(6)-fold. This CLS assay recapitulates the evolutionarily conserved features of lifespan shortening by over nutrition, lifespan extension by caloric restriction, increased stress resistance of calorically restricted cells and lifespan control by the AKT kinases. Both S. pombe AKT kinase orthologs regulate CLS: loss of sck1(+) extended lifespan in over nutrition conditions, loss of sck2(+) extended lifespan under both normal and over nutrition conditions, and loss of both genes showed that sck1(+) and sck2(+) control different longevity pathways. The longest-lived S. pombe cells showed the most efficient cell cycle exit, demonstrating that caloric restriction links these two processes. This new S. pombe CLS assay will provide a valuable tool for aging research.

Plasticity of death rates in stationary phase in Saccharomyces cerevisiae

For the species that have been most carefully studied, mortality rises with age and then plateaus or declines at advanced ages, except for yeast. Remarkably, mortality for yeast can rise, fall and rise again. In the present study we investigated (i) if this complicated shape could be modulated by environmental conditions by measuring mortality with different food media and temperature; (ii) if it is triggered by biological heterogeneity by measuring mortality in stationary phase in populations fractionated into subpopulations of young, virgin cells, and replicatively older, non-virgin cells. We also discussed the results of a staining method to measure viability instead of measuring the number of cells able to exit stationary phase and form a colony. We showed that different shapes of age-specific death rates were observed and that their appearance depended on the environmental conditions. Furthermore, biological heterogeneity explained the shapes of mortality with homogeneous populations of young, virgin cells exhibiting a simple shape of mortality in conditions under which more heterogeneous populations of older cells or unfractionated populations displayed complicated death rates. Finally, the staining method suggested that cells lost the capacity to exit stationary phase and to divide long before they died in stationary phase. These results explain a phenomenon that was puzzling because it appeared to reflect a radical departure from mortality patterns observed for other species.

How to live long and prosper: autophagy, mitochondria, and aging

Autophagy is a process of cellular self-degradation in which portions of the cytoplasm are sequestered within cytosolic double-membrane vesicles and delivered to the lysosome/vacuole. This process occurs in all eukaryotic cells and is partly a stress response; autophagy is induced during starvation and hypoxia. However, autophagy also plays a role during development and is associated with a range of diseases. Accumulating data also suggest the involvement of autophagy in aging. For example, the role of various hormones and nutrient sensing pathways in life span extension may involve autophagy. Similarly, autophagy is the primary mechanism for removing damaged organelles, such as mitochondria, which may have a direct impact on aging. Here, we review the role of autophagy, with an emphasis on the signaling pathways that are involved in regulation, and the consequences of autophagy induction with regard to aging.

Oxidative stress and chronological aging in glycogen-phosphorylase-deleted yeast

Chronological aging in yeast resembles aging in mammalian, postmitotic tissues. Such chronological aging begins with entrance into the stationary phase after the nutrients are exhausted. Many changes in metabolism take place at this moment, and survival in this phase strongly depends on oxidative-stress resistance. In this study, hypo- and hyperglycogenic phenotypes of Saccharomyces cerevisiae strains with deletions of carbohydrate-metabolism enzymes were selected, and a comparison of their chronological longevities was made. Stress sensitivity, ROS, and apoptosis markers during aging were analyzed in the emerged candidates. Among the strains that accumulated greater amounts of glycogen, the deletion of glycogen phosphorylase, gph1delta, was unique in showing a shortened life span, stress intolerance, and higher levels of ROS during its survival. The transcription of superoxide dismutase genes during survival was three- to fourfold lower in gph1delta. Extra copies of SOD1/2 counteracted the stress sensitivity and the accelerated aging of gph1delta. In conclusion, the lack of gph1 produced a rapidly aging strain, which could be attributed, at least in part, to the weakened stress resistance associated with the decreased expression of both SODs. Gph1p seems to be a candidate in a scenario that could link early metabolic changes with other targets of the stress response during stationary-phase survival.

Genomic instability is associated with natural life span variation in Saccharomyces cerevisiae

Increasing genomic instability is associated with aging in eukaryotes, but the connection between genomic instability and natural variation in life span is unknown. We have quantified chronological life span and loss-of-heterozygosity (LOH) in 11 natural isolates of Saccharomyces cerevisiae. We show that genomic instability increases and mitotic asymmetry breaks down during chronological aging. The age-dependent increase of genomic instability generally lags behind the drop of viability and this delay accounts for approximately 50% of the observed natural variation of replicative life span in these yeast isolates. We conclude that the abilities of yeast strains to tolerate genomic instability co-vary with their replicative life spans. To the best of our knowledge, this is the first quantitative evidence that demonstrates a link between genomic instability and natural variation in life span.

Protein:protein aggregation induced by protein oxidation

When the level of reactive oxygen species (ROS) in cells exceeds a genetically coded defense capacity, the cells experience damage to vital components such as DNA, proteins and lipids that leads to non-specific interactions and the production of a series of high molecular weight protein aggregates. The dynamics of oxidative stress induced aggregation were studied here using model proteins and yeast. Model proteins were oxidized at increasing ROS concentrations and analyzed using size exclusion chromatography (SEC). Changes in the SEC elution profile showed that aggregation happens in stages and protein fragments produced as a result of oxidation also give rise to aggregates. Yeast cells were stressed with hydrogen peroxide to investigate in vivo aggregation. Equal amounts from control and oxidized lysates were chromatographed on a size exclusion column and proteins of molecular weight exceeding 700 kDa were collected from both samples which were then differentially labeled using light and heavy isotope coded N-acetoxysuccinamide and mixed in a 1:1 ratio. The coded mixture was analyzed using LC/MS and peptides that appeared as singlets representing the proteins that aggregated with higher molecular mass protein complexes were identified. Twenty-five proteins were identified to be of this type. Fifteen members in this group were found to have been carbonylated. These proteins are part of the proteome known as the aggresome. The protein content of the aggresome may provide vital information for mechanistic studies targeting disease and aging.

Isc1p plays a key role in hydrogen peroxide resistance and chronological lifespan through modulation of iron levels and apoptosis

The inositolphosphosphingolipid phospholipase C (Isc1p) of Saccharomyces cerevisiae belongs to the family of neutral sphingomyelinases that generates the bioactive sphingolipid ceramide. In this work the role of Isc1p in oxidative stress resistance and chronological lifespan was investigated. Loss of Isc1p resulted in a higher sensitivity to hydrogen peroxide that was associated with an increase in oxidative stress markers, namely intracellular oxidation, protein carbonylation, and lipid peroxidation. Microarray analysis showed that Isc1p deficiency up-regulated the iron regulon leading to increased levels of iron, which is known to catalyze the production of the highly reactive hydroxyl radicals via the Fenton reaction. In agreement, iron chelation suppressed hydrogen peroxide sensitivity of isc1Delta mutants. Cells lacking Isc1p also displayed a shortened chronological lifespan associated with oxidative stress markers and aging of parental cells was correlated with a decrease in Isc1p activity. The analysis of DNA fragmentation and caspase-like activity showed that Isc1p deficiency increased apoptotic cell death associated with oxidative stress and aging. Furthermore, deletion of Yca1p metacaspase suppressed the oxidative stress sensitivity and premature aging phenotypes of isc1Delta mutants. These results indicate that Isc1p plays an important role in the regulation of cellular redox homeostasis, through modulation of iron levels, and of apoptosis.

Calorie restriction extends the chronological lifespan of Saccharomyces cerevisiae independently of the Sirtuins

Calorie restriction (CR) extends the mean and maximum lifespan of a wide variety of organisms ranging from yeast to mammals, although the molecular mechanisms of action remain unclear. For the budding yeast Saccharomyces cerevisiae reducing glucose in the growth medium extends both the replicative and chronological lifespans (CLS). The conserved NAD(+)-dependent histone deacetylase, Sir2p, promotes replicative longevity in S. cerevisiae by suppressing recombination within the ribosomal DNA locus and has been proposed to mediate the effects of CR on aging. In this study, we investigated the functional relationships of the yeast Sirtuins (Sir2p, Hst1p, Hst2p, Hst3p and Hst4p) with CLS and CR. SIR2, HST2, and HST4 were not major regulators of CLS and were not required for the lifespan extension caused by shifting the glucose concentration from 2 to 0.5% (CR). Deleting HST1 or HST3 moderately shortened CLS, but did not prevent CR from extending lifespan. CR therefore works through a Sirtuin-independent mechanism in the chronological aging system. We also show that low temperature or high osmolarity additively extends CLS when combined with CR, suggesting that these stresses and CR act through separate pathways. The CR effect on CLS was not specific to glucose. Restricting other simple sugars such as galactose or fructose also extended lifespan. Importantly, growth on nonfermentable carbon sources that force yeast to exclusively utilize respiration extended lifespan at nonrestricted concentrations and provided no additional benefit when restricted, suggesting that elevated respiration capacity is an important determinant of chronological longevity.

Mutations in theRAD27andSGS1genes differentially affect the chronological and replicative lifespan of yeast cells growing on glucose and glycerol

The Sgs1 protein from Saccharomyces cerevisiae is a member of the RecQ helicases. Defects in RecQ helicases result in premature aging phenotypes in both yeasts and humans, which appear to be promoted by replicative stress. Yeast rad27 mutants also suffer from premature aging. As the human Rad27p and Sgs1p homologs interact, a similar interaction between the yeast proteins could be important for promoting longevity in S. cerevisiae. We tested the contribution of a potential interaction between Rad27p and Sgs1p to longevity by analyzing lifespan and parameters associated with longevity in rad27 and sgs1 mutants. The carbon source supporting growth also modulated longevity as evaluated by replicative and chronological lifespan measurements. Growth on glycerol promoted chronological lifespan, while maximum replicative lifespan was obtained with glucose-supported growth. In comparison to the individual mutants, the sgs1 rad27 double mutant displayed a shortened replicative lifespan and was also more sensitive to DNA-damaging agents. In addition to promoting replicative lifespan, the activity of Rad27p was critical for achieving full chronological lifespan. The rad27 mutants exhibited increased oxidative stress levels along with an elevated spontaneous mutation rate. Removal of Sgs1p activity additionally increased the oxidative stress and spontaneous mutation rate in rad27 mutants without affecting the chronological lifespan.

Inference of transcription modification in long-live yeast strains from their expression profiles

Background

Three kinases: Sch9, PKA and TOR, are suggested to be involved in both the replicative and chronological ageing in yeast. They function in pathways whose down-regulation leads to life span extension. Several stress response proteins, including two transcription factors Msn2 and Msn4, mediate the longevity extension phenotype associated with decreased activity of either Sch9, PKA, or TOR. However, the mechanisms of longevity, especially the underlying transcription program have not been fully understood.

Results

We measured the gene expression profiles in wild type yeast and three long-lived mutants: sch9Δ, ras2Δ, and tor1Δ. To elucidate the transcription program that may account for the longevity extension, we identified the transcription factors that are systematically and significantly associated with the expression differentiation in these mutants with respect to wild type by integrating microarray expression data with motif and ChIP-chip data, respectively. Our analysis suggests that three stress response transcription factors, Msn2, Msn4 and Gis1, are activated in all the three mutants. We also identify some other transcription factors such as Fhl1 and Hsf1, which may also be involved in the transcriptional modification in the long-lived mutants.

Conclusion

Combining microarray expression data with other data sources such as motif and ChIP-chip data provides biological insights into the transcription modification that leads to life span extension. In the chronologically long-lived mutant: sch9Δ, ras2Δ, and tor1Δ, several common stress response transcription factors are activated compared with the wild type according to our systematic transcription inference.

Cell growth control: little eukaryotes make big contributions

The story of rapamycin is a pharmaceutical fairytale. Discovered as an antifungal activity in a soil sample collected on Easter Island, this macrocyclic lactone and its derivatives are now billion dollar drugs, used in, and being evaluated for, a number of clinical applications. Taking advantage of its antifungal property, the molecular Target Of Rapamycin, TOR, was first described in the budding yeast Saccharomyces cerevisiae. TORs encode large, Ser/Thr protein kinases that reside in two distinct, structurally and functionally conserved, multi-protein complexes. In yeast, these complexes coordinate many different aspects of cell growth. TOR complex 1, TORC1, promotes protein synthesis and other anabolic processes, while inhibiting macroautophagy and other catabolic and stress-response processes. TORC2 primarily regulates cell polarity, although additional readouts of this complex are beginning to be characterized. TORC1 appears to be activated by nutrient cues and inhibited by stresses and rapamycin; however, detailed mechanisms are not known. In contrast, TORC2 is insensitive to rapamycin and physiological regulators of this complex have yet to be defined. Given the unsurpassed resources available to yeast researchers, this simple eukaryote continues to contribute to our understanding of eukaryotic cell growth in general and TOR function in particular.

Targeting antioxidative signal transduction and stress response system: control of pathogenic Aspergillus with phenolics that inhibit mitochondrial function

AIMS

The aim of this study was to show whether antioxidative response systems are potentially useful molecular targets for control of Aspergillus fumigatus and Aspergillus flavus. Selected phenolic agents are used in target-gene-based bioassays to determine their impact on mitochondrial respiration.

METHODS AND RESULTS

Vanillyl acetone, vanillic acid, vanillin, cinnamic acid, veratraldehyde, m-coumaric acid (phenolic agents to which Saccharomyces cerevisiae sod2delta mutant showed sensitivity), carboxin (inhibits complex II of the mitochondrial respiratory chain), strobilurins/antimycin A (inhibits complex III of the mitochondrial respiratory chain) and fludioxonil/fenpiclonil [antifungals potentiated by mitogen-activated protein kinase (MAPK)] were examined in A. fumigatus, A. flavus and S. cerevisiae. Individual or combined application of phenolics with inhibitors of mitochondrial respiration showed some of the phenolics effectively inhibited fungal growth. Target-gene bioassays were performed using a sakAdelta (MAPK deletion) strain of A. fumigatus and a complementation analysis using the mitochondrial superoxide dismutase (Mn-SOD) gene (sodA) of A. flavus in the ortholog mutant, sod2delta, of S. cerevisiae. The results demonstrated that mitochondrial antioxidative stress system plays important roles in fungal response to antifungal agents tested.

CONCLUSIONS

Antioxidative response systems of fungi can be an efficient molecular target of phenolics for pathogen control. Combined application of phenolics with inhibitors of mitochondrial respiration can effectively suppress the growth of fungi.

SIGNIFICANCE AND IMPACT OF THE STUDY

Natural compounds that do not pose any significant medical or environmental risks could serve as useful alternatives or additives to conventional antifungals. Identifying the antioxidative response systems in other pathogens could improve methods for fungal control.

Looking for putative functions of the Leishmania cytosolic SIR2 deacetylase

During the past few years, the silent information regulator SIR2 protein family has attracted great interest due to its implication in an organism's life span extension. They bear diverse subcellular localization and play a role in transcriptional silencing and DNA repair. The biochemical reaction catalysed by these enzymes (nicotinamide adenine dinucleotide-dependant deacetylase/adenosine diphosphate-ribosyl transferase) is supposed to be linked to metabolism. Members of this protein family were described in parasitic organisms, but little information is available on potential functions of such enzymes in these organisms. In this article, we review recent information on structure and peculiar functions of SIR2s in eukaryotes, with emphasis on parasitic protozoa, particularly the Trypanosomatidae. Through the enzyme localization and the diverse substrates and by-products of the enzymatic reactions, we approach the potential pathways in which the Leishmania cytosolic SIR2 protein can be involved.

The stationary phase model of aging in yeast for the study of oxidative stress and age-related neurodegeneration

Understanding the biochemical and genetic alterations that occur during the aging of post-mitotic cells is critical for understanding the etiology of abnormalities observed during the aging of the central nervous system (CNS). While many theories for cellular aging exist, the free radical theory of aging has proved useful in explaining multiple aspects of post-mitotic cell aging, including the aging of neuronal cells. It is well established that Saccharomyces cerevisiae are an invaluable model system for exploring the regulation of aging in actively dividing cells, but increasing evidence suggests that the chronological lifespan or stationary phase model of aging in S. cerevisiae may also be useful for understanding the aging process in post-mitotic cells. Interestingly, the stationary phase model of aging in S. cerevisiae recapitulates many pathological alterations observed during neuronal aging, including evidence for increased oxidative stress and proteasome inhibition. Studies using proteins relevant to multiple neurodegenerative conditions (prion, alpha-synuclein, huntingtin) have demonstrated the utility of S. cerevisiae as a model system for understanding the genetic regulation of protein aggregation and cell death. Taken together, these data highlight the potential importance of using S. cerevisiae as a model system with which to explore the molecular basis for neuronal alterations observed in normal brain aging as well as multiple age-related diseases of the CNS.

Preadaptation to efficient respiratory maintenance is essential both for maximal longevity and the retention of replicative potential in chronologically ageing yeast

Only recently have the studies of yeast ageing started to focus on the S288c-derived strains used extensively in genomics and on the longest lifespans. Chronological longevity (stationary (G(0)) survival) of such strains is greater when cells are pre-grown on a respiratory carbon source, as compared to when they are pre-grown on glucose (the latter a respiration-repressing sugar). Prior adaptation to efficient respiratory maintenance also ensures that such chronologically aged yeast cells still display a full replicative lifespan should they reenter the cell cycle. In contrast, cells that are pre-grown on glucose exhibit marked and progressive losses of replicative potential as they age chronologically in stationary phase. Increasing the respiratory activity in glucose-grown cultures by HAP4 gene overexpression increased survival and reversed the loss of replicative potential during a subsequent stationary phase. Adaptation to efficient respiratory maintenance is therefore important, not just for maximal longevity, but also for the maintenance of a full replicative lifespan by chronologically ageing cultures of yeast. In such respiration-adapted cultures, losses of the Sch9 protein kinase or Yca1 caspase both shortened lifespan. In contrast loss of Yap1, the major transcriptional regulator of the oxidative stress response, generated a small increase in chronological lifespan in certain strain backgrounds. It would appear, therefore, that any induction of oxidative stress response genes in chronologically ageing yeast is not operating to generate an increase in longevity, even though such protective effects might be expected from the increased proxidant status of these cells over time.

Isolation of mutations synthetic-lethal to prohibitin 2 null mutants of Saccharomyces cerevisiae

Prohibitins are ubiquitous, abundant proteins found in a wide range of organisms and that have a high degree of sequence conservation. In yeast it has previously been demonstrated that prohibitin proteins form a complex and are involved in maintaining the morphological and functional integrity of mitochondria. We have used a colony-sectoring assay as a screen for mutants that are dependent upon the presence of functional Phb2p in the cell. Two classes of prohibitin dependent mutation (pbd1 and pbd2) were isolated and characterised. The effect of these mutations on replicative lifespan was determined, demonstrating that the pbd1 mutant slightly extended lifespan, whereas in contrast, the pbd2 mutation resulted in a shortening in both the mean- and the maximum-lifespan. The pbd1 mutation was also found to reduce chronological lifespan. Reducing the expression of the PHB2 gene in the pbd mutants was found to retard the rate of growth and to affect replicative lifespan. As the two mutants behave in a different manner they probably affect different aspects of prohibitin function.

Natural variation in replicative and chronological life spans of Saccharomyces cerevisiae

Natural variation in the lifespan of natural yeast populations has not been systematically investigated. Here, we have quantified the variation in the replicative and chronological life spans (RLS and CLS) in natural isolates of Saccharomyces cerevisiae and found that genotypic variation accounts for about 22% of the total variation of RLS. Strikingly, the average RLS of 14 natural isolates is about 30% longer than that of 13 laboratory strains (32 versus 21 cell divisions). As is the case for aging in mammals, there is a negative correlation between the logarithmic transformation of the initial mortality rate and the Gompertz coefficient for RLS. Thus this characteristic feature of aging is conserved from yeast to mammals. The average CLS of the natural isolates is about 7 days, significantly shorter than that of the laboratory strains. There is no correlation between RLS and CLS in natural isolates. Possible reasons for the differences between natural and laboratory strains are discussed.

Extension of chronological life span in yeast by decreased TOR pathway signaling

Chronological life span (CLS) in Saccharomyces cerevisiae, defined as the time cells in a stationary phase culture remain viable, has been proposed as a model for the aging of post-mitotic tissues in mammals. We developed a high-throughput assay to determine CLS for approximately 4800 single-gene deletion strains of yeast, and identified long-lived strains carrying mutations in the conserved TOR pathway. TOR signaling regulates multiple cellular processes in response to nutrients, especially amino acids, raising the possibility that decreased TOR signaling mediates life span extension by calorie restriction. In support of this possibility, removal of either asparagine or glutamate from the media significantly increased stationary phase survival. Pharmacological inhibition of TOR signaling by methionine sulfoximine or rapamycin also increased CLS. Decreased TOR activity also promoted increased accumulation of storage carbohydrates and enhanced stress resistance and nuclear relocalization of the stress-related transcription factor Msn2. We propose that up-regulation of a highly conserved response to starvation-induced stress is important for life span extension by decreased TOR signaling in yeast and higher eukaryotes.

Yeast AMID homologue Ndi1p displays respiration-restricted apoptotic activity and is involved in chronological aging

Apoptosis-inducing factor (AIF) and AIF-homologous mitochondrion-associated inducer of death (AMID) are both mitochondrial flavoproteins that trigger caspase-independent apoptosis. Phylogenetic analysis suggests that these two proteins evolutionarily diverge back from their common prokaryote ancestor. Compared with AIF, the proapoptotic nature of AMID and its mode of action are much less clarified. Here, we show that overexpression of yeast AMID homologue internal NADH dehydrogenase (NDI1), but not external NADH dehydrogenase (NDE1), can cause apoptosis-like cell death, and this effect can be repressed by increased respiration on glucose-limited media. This result indicates that the regulatory network of energy metabolism, in particular the cross-talk between mitochondria and the rest of the cell, is involved in Ndi1p-induced yeast cell apoptosis. The apoptotic effect of NDI1 overexpression is associated with increased production of reactive oxygen species (ROS) in mitochondria. In addition, NDI1 overexpression in sod2 background causes cell lethality in both fermentable and semifermentable media. Interruption of certain components in the electron transport chain can suppress the growth inhibition from Ndi1p overexpression. We finally show that disruption of NDI1 or NDE1 decreases ROS production and elongates the chronological life span of yeast, accompanied by the loss of survival fitness. Implication of these findings for Ndi1p-induced apoptosis is discussed.

Long-lived yeast as a model for ageing research

Yeast has essentially two lifespans: a replicative lifespan (the number of daughters produced by each dividing mother cell) and a chronological lifespan (the capacity of stationary (G0) cultures to maintain viability over time). There is a tendency now to label every investigation that addresses these lifespans as ageing research. It is, though, analyses of the longest lifespans that will be most informative about the determinants of longevity and yield results most relevant to ageing in more complex systems. This review addresses these issues and describes the ongoing studies that are now attempting to address ageing in yeast cells of maximal replicative or chronological longevity.

A role for actin in aging and apoptosis

The actin cytoskeleton is central to many cell processes including membrane trafficking and generation of cell polarity. We have identified a role for actin in cell death and in promoting longevity of the budding yeast, Saccharomyces cerevisiae. Aging in yeast appears to occur via an apoptotic-like pathway with changes including DNA fragmentation, loss of mitochondrial membrane permeability, increase in levels of ROS (reactive oxygen species) and exposure of phosphatidylserine in the outer leaflet of the plasma membrane. This pathway can be induced by alterations in actin dynamics, such that reduced dynamics correlates with increased levels of ROS and decreased viability. Conversely, increased actin dynamics correlates with low ROS levels and increased survival. Our current studies have focused on identifying pathways which couple changes in actin dynamics to cell death.

The actin cytoskeleton: a key regulator of apoptosis and ageing?

Evidence from many organisms has shown that the accumulation of reactive oxygen species (ROS) has a detrimental effect on cell well-being. High levels of ROS have been linked to programmed cell death pathways and to ageing. Recent reports have implicated changes to the dynamics of the actin cytoskeleton in the release of ROS from mitochondria and subsequent cell death.

Influence of chronological aging on the survival and nucleotide content of Saccharomyces cerevisiae cells grown in different conditions: occurrence of a high concentration of UDP-N-acetylglucosamine in stationary cells grown in 2% glucose

Saccharomyces cerevisiae cells (strain W303) grown in a minimal medium (containing 2% or 0.1% glucose) until exponential or stationary phase, were subjected to chronological aging in water, and yeast viability and nucleotide content were analyzed along several days of nutrient starvation. Cells collected in exponential phase (whether grown in the presence of 0.1% or 2% glucose) were viable up to five days and thereafter the viability decreased linearly with a half-survival rate of around eight days. ATP and other nucleoside triphosphates decreased similarly in both cases. Cells collected in stationary phase, and transferred to water, behaved differently whether grown in 0.1% or in 2% glucose, with a half-survival life of around nine and 28 days respectively. A double mutant in glycogen synthase (gsy1delta gsy2delta) and its isogenic wild-type strain, grown to stationary phase in 2% glucose, presented a similar half-survival life of around eight days. The W303 cells grown to stationary phase in the presence of 2% glucose showed a 7-fold increase of UDP-N-acetylglucosamine (UDP-GlcNAc) as compared with the level present in the cells grown in any of the other three metabolic situations. The nature of UDP-GlcNAc was established by MALDI-TOF ionization analysis. It is also worth noting that the rate of decay of NAD+ was lower than that of ATP in any of the situations here considered.

Overexpressed Sod1p acts either to reduce or to increase the lifespans and stress resistance of yeast, depending on whether it is Cu(2+)-deficient or an active Cu,Zn-superoxide dismutase

Yeast overexpressing SOD1, the gene for Cu,Zn-superoxide dismutase (Cu,Zn-Sod), was used to determine how Sod1p overexpression influences the chronological lifespan [the survival of non-dividing stationary (G0) phase cells over time], the replicative lifespan (the number of buds produced by actively dividing yeast cells) and stress resistance. Increasing the level of active Cu,Zn-Sod in yeast was found to require either growth in the presence of high copper, or the simultaneous overexpression of both SOD1 and CCS1 (the latter being the gene that encodes the chaperone dedicated to Cu(2+)-loading of Sod1p in vivo). Dual SOD1 + CCS1 overexpression elevated the levels of Cu,Zn-Sod activity six- to eight-fold in vegetative cultures. It also increased the optimized survival of stationary cells up to two-fold, showing this chronological lifespan is ultimately limited by oxidative stress. In contrast, several detrimental effects resulted when the SOD1 gene was overexpressed in the absence of either high copper or a simultaneous overexpression of CCS1. Both the chronological and the replicative lifespans were shortened; the cells displayed an abnormally high level of endogenous oxidative stress, resulting in a high rate of spontaneous mutation. Such harmful effects were all reversed through the overexpression of CCS1. It is apparent therefore that they relate to the incomplete Cu(2+)-loading of the overexpressed Sod1p, most probably accumulation of a Cu(2+)-deficient Sod1p to appreciable levels in vivo. The same events may generate the detrimental effects that are frequently, though not universally, observed when Cu,Zn-Sod overexpression is attempted in metazoans.

Genes determining yeast replicative life span in a long-lived genetic background

Here we describe the replicative life spans of more than 50 congenic Saccharomyces cerevisiae strains, each carrying a mutation previously implicated in yeast aging. This analysis provides a direct comparison, in a single, long-lived strain background, of a majority of reported yeast aging genes. Of the eleven deletion mutations previously reported to increase yeast life span, we find that deletion of FOB1, deletion of SCH9, and deletion of GPA2, GPR1, or HXK2 (three genetic models of calorie restriction) significantly enhanced longevity. In addition, over-expression of SIR2 or growth on low glucose increased life span. These results define a limited number of genes likely to regulate replicative life span in a strain-independent manner, and create a basis for future epistasis analysis to determine genetic pathways of aging.

Yeast Model Systems for Examining Nitrogen Oxide Biochemistry/Signaling

The yeast Saccharomyces cerevisiae is an ideal model system for examining fundamental nitrogen oxide biochemistry. The utility of this model system lies in both the similarities and the differences between yeast and mammalian cells. The similarities between the two systems, with regards to many of the fundamental biochemical processes, allow studies in yeast to be extrapolated to mammalian systems. On the other hand, yeast has distinct differences that allow, for example, the facile examination of O2, pH, and genetic dependencies on a number of nitrogen oxide-mediated processes. Thus, the yeast system is amenable to experimentation that is otherwise problematic or impossible in mammalian systems. Herein, we present several examples of the utility of the yeast model system for studying the intimate details of basic nitrogen oxide biochemistry.

Reserve carbohydrates maintain the viability of Saccharomyces cerevisiae cells during chronological aging

Glycogen and trehalose are well known to participate in many important cell functions, e.g., protection from stress factors, regulation of cell growth and division, spore formation. Since the aging is a complex process involving many aspects of cell metabolism, it was interesting to study the role of glycogen and trehalose in maintenance of viability of aging cells. We have revealed that cell aging is accompanied by an abrupt fall of glycogen and trehalose contents between the second and third weeks of aging. Simultaneously, we observed a decrease in the activity of glycolytic enzymes, phosphofructokinase and hexokinase. At the same time, the viability of aging cells abruptly declined. Although we found neither glycogen nor trehalose in the cells after the third week of aging, they remained viable for some time, apparently due to development of some compensatory metabolic pathways. In spite of this fact, complete death of the cells occurred by the eighth week of experiment, which confirmed irreplaceability of reserve carbohydrates in yeast cell metabolism. Possible reasons of the inability of aging cells to accumulate glycogen and trehalose are discussed in the work.

A novel assay for replicative lifespan in

The replicative lifespan of Saccharomyces cerevisiae is determined by both genetic and environmental factors. Many of the same factors determine the lifespan of metazoan animals. The lack of fast and reliable lifespan assays has limited the pace of yeast aging research. In this study we describe a novel strategy for assaying replicative lifespan in yeast, and apply it in a screening of mutants that are resistant to pro-oxidants. The assay reproduces the lifespan-shortening effects of deleting SIR2 and of growth in the presence of paraquat, a pro-oxidant. The lifespan-increasing activity of resveratrol is also reproduced. Compared to current assays, this new strategy promises to significantly increase the possible number of replicative-lifespan determinations.

Chronological aging leads to apoptosis in yeast

During the past years, yeast has been successfully established as a model to study mechanisms of apoptotic regulation. However, the beneficial effects of such a cell suicide program for a unicellular organism remained obscure. Here, we demonstrate that chronologically aged yeast cultures die exhibiting typical markers of apoptosis, accumulate oxygen radicals, and show caspase activation. Age-induced cell death is strongly delayed by overexpressing YAP1, a key transcriptional regulator in oxygen stress response. Disruption of apoptosis through deletion of yeast caspase YCA1 initially results in better survival of aged cultures. However, surviving cells lose the ability of regrowth, indicating that predamaged cells accumulate in the absence of apoptotic cell removal. Moreover, wild-type cells outlast yca1 disruptants in direct competition assays during long-term aging. We suggest that apoptosis in yeast confers a selective advantage for this unicellular organism, and demonstrate that old yeast cells release substances into the medium that stimulate survival of the clone.

Proteasome synthesis and assembly are required for survival during stationary phase

We examined the alterations in 20S proteasome homeostasis, protein oxidation, and cell viability that occur during the stationary phase or chronological model of yeast aging. Data in this report demonstrate that proteasome subunit expression is increased, proteasome composition is altered, and levels of individual proteasome proteolytic activities are elevated during stationary phase-induced aging in Saccharomyces cerevisiae. Despite such alterations, a progressive loss of proteasome-mediated protein degradation and a significant increase in protein oxidation were observed in cells maintained under stationary phase conditions. Deletion of UMP1, a gene necessary for 20S proteasome biogenesis, had no effect on cellular viability under normal growth conditions, but impaired the ability of cells to survive under stationary phase conditions. During stationary phase, the levels of oxidized protein increased more rapidly and to higher levels in the mutant lacking UMP1 than in the wild-type cells. Taken together, these data implicate a role for proteasome synthesis and altered 20S proteasome composition in maintaining viability during stationary phase, and demonstrate that even with these modifications a gradual loss of proteasome-mediated protein degradation occurs during stationary phase-induced aging. These data also suggest a role for impaired proteasome-mediated protein degradation in increased protein oxidation and cell death observed during the aging of eukaryotic cells.

Biodemographic trajectories of age-specific reproliferation from stationary phase in the yeast Saccharomyces cerevisiae seem multiphasic

Ageing is usually seen as a monotonic decline of functions and survival. However, recent studies reported that age-specific mortality rates increased and then leveled off or even declined at later ages in several species including humans. Preliminary data using the yeast, Saccharomyces cerevisiae, demonstrated an even more complicated, non-monotonic pattern of reproliferation after stationary phase (i.e. the ability of a cell to exit stationary phase and form a colony). In the present article, we conducted a study of the age-specific reproliferation rates of yeast populations. Stationary phase yeast cells were maintained in water and the reproliferation rates were estimated by the number of yeast able to exit stationary phase on rich growth media. We showed that the age-specific reproliferation rates in yeast seem to rise, fall and rise again. Furthermore, we observed this pattern in different experiments and in different genotypes and established that this pattern was not due to genetic heterogeneity of the populations.

"Sleeping beauty": quiescence in Saccharomyces cerevisiae

The cells of organisms as diverse as bacteria and humans can enter stable, nonproliferating quiescent states. Quiescent cells of eukaryotic and prokaryotic microorganisms can survive for long periods without nutrients. This alternative state of cells is still poorly understood, yet much benefit is to be gained by understanding it both scientifically and with reference to human health. Here, we review our knowledge of one "model" quiescent cell population, in cultures of yeast grown to stationary phase in rich media. We outline the importance of understanding quiescence, summarize the properties of quiescent yeast cells, and clarify some definitions of the state. We propose that the processes by which a cell enters into, maintains viability in, and exits from quiescence are best viewed as an environmentally triggered cycle: the cell quiescence cycle. We synthesize what is known about the mechanisms by which yeast cells enter into quiescence, including the possible roles of the protein kinase A, TOR, protein kinase C, and Snf1p pathways. We also discuss selected mechanisms by which quiescent cells maintain viability, including metabolism, protein modification, and redox homeostasis. Finally, we outline what is known about the process by which cells exit from quiescence when nutrients again become available.

Oxidative damage to specific proteins in replicative and chronological-aged Saccharomyces cerevisiae: common targets and prevention by calorie restriction

Oxidative modifications of cellular components have been described as one of the main contributions to aged phenotype. In Saccharomyces cerevisiae, two distinct life spans can be considered, replicative and chronological. The relationship between both aging models is still not clear despite suggestions that these phenomena may be related. In this work, we show that replicative and chronological-aged yeast cells are affected by an oxidative stress situation demonstrated by increased protein carbonylation when compared with young cells. The data on the identification of these oxidatively modified proteins gives clues to better understand cellular dysfunction that occurs during aging. Strikingly, although in both aging models metabolic differences are important, major targets are almost the same. Common targets include stress resistance proteins (Hsp60 and Hsp70) and enzymes involved in glucose metabolism such as enolase, glyceraldehydes-3-P dehydrogenase, fructose-1,6-biphosphate aldolase, pyruvate decarboxylase, and alcohol dehydrogenase. In both aging models, calorie restriction results in decreased damage to these proteins. In addition, chronological-aged cells grown under glucose restriction displayed lowered levels of lipid peroxidation product lipofuscin. Intracellular iron concentration is kept almost unchanged, whereas in non-restricted cells, the values increase up 4-5 times. The pro-oxidant effects of such increased iron concentration would account for the damage observed. Also, calorie-restricted cells show undamaged catalase, which clearly appears carbonylated in cells grown at a high glucose concentration. These results may explain lengthening of the viability of chronological-aged cells and could have an important role in replicative life span extension by calorie restriction.

Expression of the human ferritin light chain in a frataxin mutant yeast affects ageing and cell death

Ferritin is one of the major eukaryotic proteins involved in regulating iron metabolism and maintaining iron homeostasis. However, Saccaromyces cerevisiae is an exception, possessing no ferritin and using other means to store excess iron. The only potential iron storage protein identified in yeast so far is the homologue of human frataxin (YFH1p). In this study, we found that dysfunction of yeast frataxin shortens mean lifespan by 49% compared to the WT control. Interestingly, the human ferritin L gene can, at least partially, complement the function of yeast frataxin, extending lifespan and protecting cells from death induced by oxidative stress or excess iron. Our findings indicate that ferritin L can perform functions in yeast that are similar to its functions in mammals, and suggest that common mechanisms may exist for preventing iron and oxidative damage in single- and multi-cellular eukaryotic organisms. Clearly, elucidation of the function of human ferritin in yeast would help in gaining a better understanding the molecular basis of iron storage diseases.

A role for the actin cytoskeleton in cell death and aging in yeast

Several determinants of aging, including metabolic capacity and genetic stability, are recognized in both yeast and humans. However, many aspects of the pathways leading to cell death remain to be elucidated. Here we report a role for the actin cytoskeleton both in cell death and in promoting longevity. We have analyzed yeast strains expressing mutants with either increased or decreased actin dynamics. We show that decreased actin dynamics causes depolarization of the mitochondrial membrane and an increase in reactive oxygen species (ROS) production, resulting in cell death. Important, however, is the demonstration that increasing actin dynamics, either by a specific actin allele or by deletion of a gene encoding the actin-bundling protein Scp1p, can increase lifespan by over 65%. Increased longevity appears to be due to these cells producing lower than wild-type levels of ROS. Homology between Scp1p and mammalian SM22/transgelin, which itself has been isolated in senescence screens, suggests a conserved mechanism linking aging to actin stability.