Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae

Trehalose and glycogen accumulation is related to the duration of the G1 phase of Saccharomyces cerevisiae

Several factors may control trehalose and glycogen synthesis, like the glucose flux, the growth rate, the intracellular glucose-6-phosphate level and the glucose concentration in the medium. Here, the possible relation of these putative inducers to reserve carbohydrate accumulation was studied under well-defined growth conditions in nitrogen-limited continuous cultures. We showed that the amounts of accumulated trehalose and glycogen were regulated by the growth rate imposed on the culture, whereas other implicated inducers did not exhibit a correlation with reserve carbohydrate accumulation. Trehalose accumulation was induced at a dilution rate (D)</=0.10 h(-1), whereas glycogen accumulation gradually increased at decreasing growth rates. The growth rate dependency of trehalose accumulation was supported by studies in cells overexpressing the G(1)-cyclin CLN3. The trehalose level appeared to be dependent on the duration of the G(1) phase, as trehalose was only accumulated at a G(1) phase duration of more than 5 h in both wild-type and CLN3-overexpressing cells. On the other hand, the glycogen level was reduced by CLN3 overexpression in a cell cycle-independent manner. A possible regulatory mechanism that links trehalose and glycogen accumulation to the growth rate is discussed.

Sip2, an N-myristoylated beta subunit of Snf1 kinase, regulates aging in Saccharomyces cerevisiae by affecting cellular histone kinase activity, recombination at rDNA loci, and silencing

Saccharomyces cerevisiae has evolved a number of mechanisms for sensing glucose. In the present study we examine the mechanism by which one of these pathways, involving Snf1, regulates cellular aging. Snf1 is a heterotrimer composed of a catalytic alpha subunit (Snf1p) that phosphorylates target proteins at Ser/Thr residues, an activating gamma subunit (Snf4p), and a beta subunit (Sip1p, Sip2p, or Gal83). We previously showed that forced expression of Snf1p or loss of Sip2p, but not the other beta subunits, causes accelerated aging, while removal of Snf4p extends life span (Ashrafi, K., Lin, S. S., Manchester, J. K., and Gordon, J. I. (2000) Genes Dev. 14, 1872-1885). We now demonstrate that in wild type cells, there is an age-associated shift in Sip2p from the plasma membrane to the cytoplasm, a prominent redistribution of Snf4p from the plasma membrane to the nucleus, a modest increase in nuclear Snf1p, and a concomitant increase in cellular Snf1 histone H3 kinase activity. Covalent attachment of myristate to the N-terminal Gly of Sip2p is essential for normal cellular life span. When plasma membrane association of Sip2p is abolished by a mutation that blocks its N-myristoylation, Snf4p is shifted to the nucleus. Rapidly aging sip2 Delta cells have higher levels of histone H3 kinase activity than their generation-matched isogenic wild type counterparts. Increased Snf1 activity is associated with augmented recombination at rDNA loci, plus desilencing at sites affected by Snf1-catalyzed Ser(10) phosphorylation of histone H3 (the INO1 promoter plus targets of the transcription factor Adr1p). The rapid-aging phenotype of sip2 Delta cells is fully rescued by blocking recombination at rDNA loci with a fob1 Delta allele; rescue is not accompanied by amelioration of an age-associated shift toward gluconeogenesis and glucose storage. Together, these findings suggest that Sip2p acts as a negative regulator of nuclear Snf1 activity in young cells by sequestering its activating gamma subunit at the plasma membrane and that loss of Sip2p from the plasma membrane to the cytoplasm in aging cells facilities Snf4p entry into the nucleus so that Snf1 can modify chromatin structure.

Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae

We have investigated the role of 3',5'-cyclic-adenosine-monophosphate (cAMP) in mediating the coupling between energy metabolism and cell cycle progression in both synchronous cultures and oscillating continuous cultures of Saccharomyces cerevisiae. For the first time, a peak in intracellular cAMP was shown to precede the observed breakdown of trehalose and glycogen during cell cycle-related oscillations. Measurements in synchronous cultures demonstrated that this peak can be associated with the cell cycle dynamics of cAMP under conditions of glucose-limited growth, which was found to differ significantly from that observed in synchronous glucose-repressed cultures. Our results support the notion that cAMP plays a major role in mediating the integration of energy metabolism and cell cycle progression, both in the single cell and during cell cycle-related oscillations in continuous culture, respectively. Evidence is presented that the dynamic behaviour of intracellular cAMP during the cell cycle is modulated depending on nutrient supply. The implications of these findings regarding the role of cAMP in regulating cell cycle progression and energy metabolism are discussed.

Proteomic response to physiological fermentation stresses in a wild-type wine strain of Saccharomyces cerevisiae

We report a study on the adaptive response of a wild-type wine Saccharomyces cerevisiae strain, isolated from natural spontaneous grape must, to mild and progressive physiological stresses due to fermentation. We observed by two-dimensional electrophoresis how the yeast proteome changes during glucose exhaustion, before the cell enters its complete stationary phase. On the basis of their identification, the proteins representing the S. cerevisiae proteomic response to fermentation stresses were divided into three classes: repressed proteins, induced proteins and autoproteolysed proteins. In an overall view, the proteome adaptation of S. cerevisiae at the time of glucose exhaustion seems to be directed mainly against the effects of ethanol, causing both hyperosmolarity and oxidative responses. Stress-induced autoproteolysis is directed mainly towards specific isoforms of glycolytic enzymes. Through the use of a wild-type S. cerevisiae strain and PMSF, a specific inhibitor of vacuolar proteinase B, we could also distinguish the specific contributions of the vacuole and the proteasome to the autoproteolytic process.

Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation

The transcriptome of a wine yeast was monitored throughout an alcoholic fermentation under conditions mimicking an enological environment. Major changes in gene expression occurred during fermentation, affecting more than 2000 genes, as the yeast adapted to changing nutritional, environmental and physiological conditions. The genes of many pathways are regulated in a highly coordinated manner, and genes involved in the key metabolic pathways of fermentation are strongly expressed. We showed that, during fermentation of a synthetic medium mimicking a natural must in which growth arrest was caused by nitrogen exhaustion, entry into the stationary phase triggered major transcriptional reprogramming. Many TOR target genes involved in nitrogen utilization or other functions are induced at this stage, suggesting that this signalling pathway plays a critical role in changes in gene expression in response to nitrogen depletion. Entry into stationary phase is a key physiological event and is followed by a general stress response. The superimposition of multiple stresses, including starvation and ethanol stress, gives rise to a unique stress response, involving hundreds of genes encoding proteins involved in various cellular processes, many of unknown function.

Carbohydrate cycling in micro-organisms: what can (13)C-NMR tell us?

The extension of (13)C-nuclear magnetic resonance (NMR) techniques to study cellular metabolism over recent years has provided valuable data supporting the occurrence, diversity and extent of carbon cycling in the carbohydrate metabolism of micro-organisms. The occurrence of such cycles, resulting from the simultaneous operation of different and sometimes opposite individual steps, is inherently related to the network organisation of cellular metabolism. These cycles are tentatively classified here as 'reversibility', 'metabolic' and 'substrate' cycles on the basis of their balance in carbon and cofactors. Current hypotheses concerning the physiological relevance of carbohydrate cycles are discussed in light of the (13)C-NMR data. They most likely represent system-level mechanisms for coherent and timely partitioning of carbon resources to fit with the various biosynthetic, energetic or redox needs of cells and/or additional strategies in the adaptive capacity of micro-organisms to face variation in environmental conditions.

Glycogen synthase: towards a minimum catalytic unit?

Classically, alpha-1,4-glucan synthases have been divided into two families, animal/fungal glycogen synthases (GS) and bacterial/plant starch synthases (G(S)S), according to differences in sequence, sugar donor specificity and regulatory mechanisms. Detailed sequence analysis, predicted secondary structure comparison and threading analysis show that these two families are structurally related and that some domains of GSs were acquired to meet regulatory requirements. Archaeal G(S)S present structural and functional features that are conserved in one, the other or both families. Therefore, they are the link between GS and G(S)S and harbor the minimal sequence and structural features that constitute the minimum catalytic unit of the alpha-1,4-glucan synthase superfamily.

Sgt1p contributes to cyclic AMP pathway activity and physically interacts with the adenylyl cyclase Cyr1p/Cdc35p in budding yeast

Sgt1p is a highly conserved eucaryotic protein that is required for both SCF (Skp1p/Cdc53p-Cullin-F-box)-mediated ubiquitination and kinetochore function in yeast. We show here that Sgtlp is also involved in the cyclic AMP (cAMP) pathway in Saccharomyces cerevisiae. SGT1 is an allele-specific suppressor of cdc35-1, a thermosensitive mutation in the leucine-rich repeat domain of the adenylyl cyclase Cyrlp/Cdc35p. We demonstrate that Sgt1p and Cyrlp/Cdc35p physically interact and that the activity of the cAMP pathway is affected in an sgt1 conditional mutant. Sequence analysis suggests that Sgtlp has features of a cochaperone. Thus, Sgt1p is a novel activator of adenylyl cyclase in S. cerevisiae and may function in the assembly or the conformational activation of specific multiprotein complexes.

The genome-wide expression response to telomerase deletion in Saccharomyces cerevisiae

Loss of the protective function of telomeres has previously been hypothesized to cause a DNA damage response. Here, we report a genome-wide expression response, the telomerase deletion response (TDR), that occurs when telomeres can no longer be maintained by telomerase. The TDR shares features with other DNA damage responses and the environmental stress response. Unexpectedly, another feature of the TDR is the up-regulation of energy production genes, accompanied by a proliferation of mitochondria. Finally, a discrete set of genes, the "telomerase deletion signature", is uniquely up-regulated in the TDR but not under other conditions of stress and DNA damage that have been reported. The telomerase deletion signature genes define new candidates for involvement in cellular responses to altered telomere structure or function.

Osmotic stress signaling and osmoadaptation in yeasts

The ability to adapt to altered availability of free water is a fundamental property of living cells. The principles underlying osmoadaptation are well conserved. The yeast Saccharomyces cerevisiae is an excellent model system with which to study the molecular biology and physiology of osmoadaptation. Upon a shift to high osmolarity, yeast cells rapidly stimulate a mitogen-activated protein (MAP) kinase cascade, the high-osmolarity glycerol (HOG) pathway, which orchestrates part of the transcriptional response. The dynamic operation of the HOG pathway has been well studied, and similar osmosensing pathways exist in other eukaryotes. Protein kinase A, which seems to mediate a response to diverse stress conditions, is also involved in the transcriptional response program. Expression changes after a shift to high osmolarity aim at adjusting metabolism and the production of cellular protectants. Accumulation of the osmolyte glycerol, which is also controlled by altering transmembrane glycerol transport, is of central importance. Upon a shift from high to low osmolarity, yeast cells stimulate a different MAP kinase cascade, the cell integrity pathway. The transcriptional program upon hypo-osmotic shock seems to aim at adjusting cell surface properties. Rapid export of glycerol is an important event in adaptation to low osmolarity. Osmoadaptation, adjustment of cell surface properties, and the control of cell morphogenesis, growth, and proliferation are highly coordinated processes. The Skn7p response regulator may be involved in coordinating these events. An integrated understanding of osmoadaptation requires not only knowledge of the function of many uncharacterized genes but also further insight into the time line of events, their interdependence, their dynamics, and their spatial organization as well as the importance of subtle effects.

Systematic identification of the genes affecting glycogen storage in the yeast Saccharomyces cerevisiae: implication of the vacuole as a determinant of glycogen level

At the onset of nutrient limitation, the yeast Saccharomyces cerevisiae synthesizes glycogen to serve as a carbon and energy reserve. We undertook a systematic survey for the genes that affect glycogen accumulation by taking advantage of the strain deletion set generated by the Saccharomyces Genome Deletion Project. The strain collection analyzed contained some 4600 diploid homozygous null deletants, representing approximately 88% of all viable haploid disruptants. We identified 324 strains with low and 242 with elevated glycogen stores, accounting for 12.4% of the genes analyzed. The screen was validated by the identification of many of the genes known already to influence glycogen accumulation. Many of the mutants could be placed into coherent families. For example, 195 or 60% of the hypoaccumulators carry mutations linked to respiratory function, a class of mutants well known to be defective in glycogen storage. The second largest group consists of approximately 60 genes involved in vesicular trafficking and vacuolar function, including genes encoding 13 of 17 proteins involved in the structure or assembly of the vacuolar ATPase. These data are consistent with our recent findings that the process of autophagy has a significant impact on glycogen storage (Wang, Z., Wilson, W. A., Fujino, M. A., and Roach, P. J. (2001) Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p. Mol. Cell. Biol. 21, 5742-5752). Autophagy delivers glycogen to the vacuole, and we propose that the impaired vacuolar function associated with ATPase mutants (vma10 or vma22) results in reduced degradation and subsequent hyperaccumulation of glycogen.

Ultradian rhythm of trehalose levels coupled to heat resistance in continuous cultures of the yeast Saccharomyces cerevisiae

Heat resistance appears to cycle in concert with energy metabolism in continuous culture of the yeast Saccharomyces cerevisiae. To study the mechanism of this oscillation, the authors first examined if heat shock proteins (Hsps) are involved. Neither the protein levels of major Hsps nor the expression of the beta-galactosidase gene as a reporter under the control of the promoter carrying heat-shock element oscillated during the metabolic oscillation. The level of trehalose in yeast cycled with the same periodicity, as did energy metabolism. This oscillation was not found in a GTS1-deleted mutant that also did not show cyclic changes in heat resistance. These results suggest that heat resistance oscillation is induced by fluctuations in trehalose level and not by an oscillatory expression of Hsps. The increase in trehalose began at the start of the respiro-fermentative phase and the decrease began after the elevation of the cyclic adenosine monophosphate (cAMP) level. The authors hypothesize that the synthesis of trehalose parallels the activation of the glycolytic pathway and that trehalose is degraded by trehalase activated by cAMP coupled with the metabolic oscillation in the continuous culture of yeast.

The GCR1 gene function is essential for glycogen and trehalose metabolism in Saccharomyces cerevisiae

Trehalose (Tre) and glycogen (Glg) are synthesized in response to unfavorable growth conditions from glycolytic intermediates in Saccharomyces cerevisiae. Transcription of the glycolytic genes is activated by the Gcr1p complex, the DNA binding transcription factor that directly associates with the CT-box sequences on the promoter region of the glycolytic genes. gcr1 mutant yeast cells cannot utilize glucose effectively. Glg and Tre levels in stationary-phase gcr1 mutant yeast cells were 20-50% of those in the wild-type strain. Likewise, stress-induced accumulation of Tre and Glg in gcr1 mutant cells was significantly lower than in the wild type. In addition, both the synthesis and the degradation of Tre and Glg are very slow in the gcr1 mutant. It seems that Gcr1p function is essential for the coordinated regulation of glycolysis, Tre and Glg metabolism in S. cerevisiae.

Genomic analyses of anaerobically induced genes in Saccharomyces cerevisiae: functional roles of Rox1 and other factors in mediating the anoxic response

DNA arrays were used to investigate the functional role of Rox1 in mediating acclimatization to anaerobic conditions in Saccharomyces cerevisiae. Multiple growth conditions for wild-type and rox1 null strains were used to identify open reading frames with a statistically robust response to this repressor. These results were compared to those obtained for a wild-type strain in response to oxygen availability. Transcripts of nearly one-sixth of the genome were differentially expressed (P < 0.05) with respect to oxygen availability, the majority (>65%) being down-regulated under anoxia. Of the anaerobically induced genes, about one-third (106) contain putative Rox1-binding sites in their promoters and were significantly (P < 0.05) up-regulated in the rox1 null strains under aerobiosis. Additional promoter searches revealed that nearly one-third of the anaerobically induced genes contain an AR1 site(s) for the Upc2 transcription factor, suggesting that Upc2 and Rox1 regulate the majority of anaerobically induced genes in S. cerevisiae. Functional analyses indicate that a large fraction of the anaerobically induced genes are involved in cell stress (approximately 1/3), cell wall maintenance (approximately 1/8), carbohydrate metabolism (approximately 1/10), and lipid metabolism (approximately 1/12), with both Rox1 and Upc2 predominating in the regulation of this latter group and Upc2 predominating in cell wall maintenance. Mapping the changes in expression of functional regulons onto metabolic pathways has provided novel insight into the role of Rox1 and other trans-acting factors in mediating the physiological response of S. cerevisiae to anaerobic conditions.

The yeast cyclins Pc16p and Pc17p are involved in the control of glycogen storage by the cyclin-dependent protein kinase Pho85p

Pho85p is a yeast cyclin-dependent protein kinase (Cdk) that can interact with 10 cyclins (Pcls) to form multiple protein kinases. The functions of most of the Pcls, including Pc16p and Pc17p, are poorly defined. We report here that Pc16p and Pc17p are involved in the metabolism of the branched storage polysaccharide glycogen under certain conditions and deletion of PCL6 and PCL7 restores glycogen accumulation to a snf1 pcl8 pcl10 triple mutant, paradoxically activating both glycogen synthase and phosphorylase. Pho85p thus affects glycogen accumulation through multiple Cdks composed of different cyclin partners.

Efficacy of chitosan, carvacrol, and a hydrogen peroxide-based biocide against foodborne microorganisms in suspension and adhered to stainless steel

The ability of natural compounds to inactivate foodborne organisms adhered to surfaces was investigated with the ultimate aim of replacing synthetic biocides by more environmentally friendly, natural alternatives. The antimicrobial efficacy of 0.5, 1.0, and 2.0% chitosan and Spor-Klenz RTU (a commercial biocide based on hydrogen peroxide and peroxyacetic acid) and 0.5, 1.25, and 2.0 mM carvacrol was determined at 20 degrees C against Listeria monocytogenes, Salmonella enterica serovar Typhimurium, Staphylococcus aureus, and Saccharomyces cerevisiae adhered to stainless steel disks. Treatment with up to 2.0% chitosan reduced the viable cell count in the microbial films of the four test organisms by 2.4, 1.8, 2.3, and 0.9 log CFU/test surface (t.s.), respectively. By contrast, planktonic counts of the same organisms were reduced by 0.8 to 1.7 log CFU/ml at 2.0% chitosan. Treatment with 2 mM carvacrol reduced the viable counts of adhered listeriae, salmonellae, and yeasts by 2 to 3 log CFU/t.s. but S. aureus counts were reduced by only 0.9 log CFU/t.s. The efficacy of any single compound was species specific. In the case of microbial films prepared using listeriae and salmonellae, Spor-Klenz RTU was most biocidal, followed by carvacrol and then chitosan. However, dried films of S. aureus were most sensitive to chitosan and relatively resistant to carvacrol and Spor-Klenz RTU. By contrast, yeast films were most sensitive to carvacrol and least sensitive to chitosan. It was concluded that carvacrol and chitosan may have potential for use as natural biocides although optimization of conditions would be necessary.

Enhanced gluconeogenesis and increased energy storage as hallmarks of aging in Saccharomyces cerevisiae

A relationship between life span and cellular glucose metabolism has been inferred from genetic manipulations and caloric restriction of model organisms. In this report, we have used the Snf1p glucose-sensing pathway of Saccharomyces cerevisiae to explore the genetic and biochemical linkages between glucose metabolism and aging. Snf1p is a serine/threonine kinase that regulates cellular responses to glucose deprivation. Loss of Snf4p, an activator of Snf1p, extends generational life span whereas loss of Sip2p, a presumed repressor of the kinase, causes an accelerated aging phenotype. An annotated data base of global age-associated changes in gene expression in isogenic wild-type, sip2Delta, and snf4Delta strains was generated from DNA microarray studies. The transcriptional responses suggested that gluconeogenesis and glucose storage increase as wild-type cells age, that this metabolic evolution is exaggerated in rapidly aging sip2Delta cells, and that it is attenuated in longer-lived snf4Delta cells. To test this hypothesis directly, we applied microanalytic biochemical methods to generation-matched cells from each strain and measured the activities of enzymes and concentrations of metabolites in the gluconeogenic, glycolytic, and glyoxylate pathways, as well as glycogen, ATP, and NAD(+). The sensitivity of the assays allowed comprehensive biochemical profiling to be performed using aliquots of the same cell populations employed for the transcriptional profiling. The results provided additional evidence that aging in S. cerevisiae is associated with a shift away from glycolysis and toward gluconeogenesis and energy storage. They also disclosed that this shift is forestalled by two manipulations that extend life span, caloric restriction and genetic attenuation of the normal age-associated increase in Snf1p activity. Together, these findings indicate that Snf1p activation is not only a marker of aging but also a candidate mediator, because a shift toward energy storage over expenditure could impact myriad aspects of cellular maintenance and repair.

Antagonistic controls of autophagy and glycogen accumulation by Snf1p, the yeast homolog of AMP-activated protein kinase, and the cyclin-dependent kinase Pho85p

In the yeast Saccharomyces cerevisiae, glycogen is accumulated as a carbohydrate reserve when cells are deprived of nutrients. Yeast mutated in SNF1, a gene encoding a protein kinase required for glucose derepression, has diminished glycogen accumulation and concomitant inactivation of glycogen synthase. Restoration of synthesis in an snf1 strain results only in transient glycogen accumulation, implying the existence of other SNF1-dependent controls of glycogen storage. A genetic screen revealed that two genes involved in autophagy, APG1 and APG13, may be regulated by SNF1. Increased autophagic activity was observed in wild-type cells entering the stationary phase, but this induction was impaired in an snf1 strain. Mutants defective for autophagy were able to synthesize glycogen upon approaching the stationary phase, but were unable to maintain their glycogen stores, because subsequent synthesis was impaired and degradation by phosphorylase, Gph1p, was enhanced. Thus, deletion of GPH1 partially reversed the loss of glycogen accumulation in autophagy mutants. Loss of the vacuolar glucosidase, SGA1, also protected glycogen stores, but only very late in the stationary phase. Gph1p and Sga1p may therefore degrade physically distinct pools of glycogen. Pho85p is a cyclin-dependent protein kinase that antagonizes SNF1 control of glycogen synthesis. Induction of autophagy in pho85 mutants entering the stationary phase was exaggerated compared to the level in wild-type cells, but was blocked in apg1 pho85 mutants. We propose that Snf1p and Pho85p are, respectively, positive and negative regulators of autophagy, probably via Apg1 and/or Apg13. Defective glycogen storage in snf1 cells can be attributed to both defective synthesis upon entry into stationary phase and impaired maintenance of glycogen levels caused by the lack of autophagy.

Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast

Starvation for amino acids induces Gcn4p, a transcriptional activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. In an effort to identify all genes regulated by Gcn4p during amino acid starvation, we performed cDNA microarray analysis. Data from 21 pairs of hybridization experiments using two different strains derived from S288c revealed that more than 1,000 genes were induced, and a similar number were repressed, by a factor of 2 or more in response to histidine starvation imposed by 3-aminotriazole (3AT). Profiling of a gcn4Delta strain and a constitutively induced mutant showed that Gcn4p is required for the full induction by 3AT of at least 539 genes, termed Gcn4p targets. Genes in every amino acid biosynthetic pathway except cysteine and genes encoding amino acid precursors, vitamin biosynthetic enzymes, peroxisomal components, mitochondrial carrier proteins, and autophagy proteins were all identified as Gcn4p targets. Unexpectedly, genes involved in amino acid biosynthesis represent only a quarter of the Gcn4p target genes. Gcn4p also activates genes involved in glycogen homeostasis, and mutant analysis showed that Gcn4p suppresses glycogen levels in amino acid-starved cells. Numerous genes encoding protein kinases and transcription factors were identified as targets, suggesting that Gcn4p is a master regulator of gene expression. Interestingly, expression profiles for 3AT and the alkylating agent methyl methanesulfonate (MMS) overlapped extensively, and MMS induced GCN4 translation. Thus, the broad transcriptional response evoked by Gcn4p is produced by diverse stress conditions. Finally, profiling of a gcn4Delta mutant uncovered an alternative induction pathway operating at many Gcn4p target genes in histidine-starved cells.