Ethanol-sensitive mutants of Saccharomyces cerevisiae

RNA metabolism is the primary target of formamide in vivo

The synthesis, processing and function of coding and non-coding RNA molecules and their interacting proteins has been the focus of a great deal of research that has boosted our understanding of key molecular pathways that underlie higher order events such as cell cycle control, development, innate immune response and the occurrence of genetic diseases. In this study, we have found that formamide preferentially weakens RNA related processes in vivo. Using a non-essential Schizosaccharomyces pombe gene deletion collection, we identify deleted loci that make cells sensitive to formamide. Sensitive deletions are significantly enriched in genes involved in RNA metabolism. Accordingly, we find that previously known temperature-sensitive splicing mutants become lethal in the presence of the drug under permissive temperature. Furthermore, in a wild type background, splicing efficiency is decreased and R-loop formation is increased in the presence of formamide. In addition, we have also isolated 35 formamide-sensitive mutants, many of which display remarkable morphology and cell cycle defects potentially unveiling new players in the regulation of these processes. We conclude that formamide preferentially targets RNA related processes in vivo, probably by relaxing RNA secondary structures and/or RNA-protein interactions, and can be used as an effective tool to characterize these processes.

Transcriptional changes associated with ethanol tolerance in Saccharomyces cerevisiae

Saccharomyces spp. are widely used for ethanol production; however, fermentation productivity is negatively affected by the impact of ethanol accumulation on yeast metabolic rate and viability. This study used microarray and statistical two-way ANOVA analysis to compare and evaluate gene expression profiles of two previously generated ethanol-tolerant mutants, CM1 and SM1, with their parent, Saccharomyces cerevisiae W303-1A, in the presence and absence of ethanol stress. Although sharing the same parentage, the mutants were created differently: SM1 by adaptive evolution involving long-term exposure to ethanol stress and CM1 using chemical mutagenesis followed by adaptive evolution-based screening. Compared to the parent, differences in the expression levels of genes associated with a number of gene ontology categories in the mutants suggest that their improved ethanol stress response is a consequence of increased mitochondrial and NADH oxidation activities, stimulating glycolysis and other energy-yielding pathways. This leads to increased activity of energy-demanding processes associated with the production of proteins and plasma membrane components, which are necessary for acclimation to ethanol stress. It is suggested that a key function of the ethanol stress response is restoration of the NAD(+)/NADH redox balance, which increases glyceraldehyde-3-phosphate dehydrogenase activity, and higher glycolytic flux in the ethanol-stressed cell. Both mutants achieved this by a constitutive increase in carbon flux in the glycerol pathway as a means of increasing NADH oxidation.

Adaptation of yeast cell membranes to ethanol

A highly ethanol-tolerant Saccharomyces wine strain is able, after growth in the presence of ethanol, to efficiently improve the ethanol tolerance of its membrane. A less-tolerant Saccharomyces laboratory strain, however, is unable to adapt its membrane to ethanol. Furthermore, after growth in the presence of ethanol, the membrane of the latter strain becomes increasingly sensitive, although this is a reversible process. Reversion to a higher tolerance occurs only after the addition of an energy source and does not take place in the presence of cycloheximide.

Effect of continued exposition to ethanol on activity of the ammonium and fructose transport systems in Saccharomyces cerevisiae var. ellipsoideus

Ethanol and cycloheximide inhibited the function of the ammonium transport system in growing cultures of Saccharomyces cerevisiae var. ellipsoideus measured as methylamine uptake. The effect was reversible with ethanol and irreversible with the antibiotic. The kinetic data are consistent with a reduction of the number of active carrier molecules located in the plasma membrane. In contrast, neither ethanol nor cycloheximide affected the specific rate of fructose uptake.

Ethanol stress stimulates the Ca2+-mediated calcineurin/Crz1 pathway in Saccharomyces cerevisiae

Environmental stimuli elicit a stress response, which helps to maintain cell survival. In budding yeast Saccharomyces cerevisiae, environmental cues can activate calcineurin, a highly conserved Ca2+-- and calmodulin-dependent protein phosphatase. Calcineurin dephosphorylates the transcription factor Crz1, leading to accumulation of Crz1 in the nuclei and expression of stress responsive genes under the control of a calcineurin-dependent response element (CDRE). Ethanol is the final product of sugar fermentation by yeast, and thus a frequently encountered yeast stressor. However, adaptation of yeast to ethanol stress is poorly understood. In this study, we show that ethanol stimulates calcineurin-dependent nuclear localization of Crz1 and CDRE-dependent gene expression. Moreover, cells in which CRZ1 is deleted exhibit defective adaptation to ethanol stress, while a multicopy plasmid of CRZ1 confers an increased level of adaptive stress tolerance to ethanol. Taken together, the results indicate that ethanol activates the calcineurin/Crz1 pathway and that CRZ1 is crucial for cell survival under ethanol-induced stress.

Disruption ofURA7 andGAL6 improves the ethanol tolerance and fermentation capacity ofSaccharomyces cerevisiae

Screening of the homozygous diploid yeast deletion pool of 4741 non-essential genes identified two null mutants (Deltaura7 and Deltagal6) that grew faster than the wild-type strain in medium containing 8% v/v ethanol. The survival rate of the gal6 disruptant in 10% ethanol was higher than that of the wild-type strain. On the other hand, the glucose consumption rate of the ura7 disruptant was better than that of the wild-type strain in buffer containing ethanol. Both disruptants were more resistant to zymolyase, a yeast lytic enzyme containing mainly beta-1,3-glucanase, indicating that the integrity of the cell wall became more resistance to ethanol stress. The gal6 disruptant was also more resistant to Calcofluor white, but the ura7 disruptant was more sensitive to Calcofluor white than the wild-type strain. Furthermore, the mutant strains had a higher content of oleic acid (C18 : 1) in the presence of ethanol compared to the wild-type strain, suggesting that the disruptants cope with ethanol stress not only by modifying the cell wall integrity but also the membrane fluidity. When the cells were grown in medium containing 5% ethanol at 15 degrees C, the gal6 and ura7 disruptants showed 40% and 14% increases in the glucose consumption rate, respectively.

Asr1, an alcohol-responsive factor of Saccharomyces cerevisiae, is dispensable for alcoholic fermentation

Yeast Asr1 is the first reported protein whose intracellular distribution changes specifically in response to alcohol (Betz et al. (2004) J Biol Chem 279:28174-28181). It was reported that Asr1 is required for tolerance to alcohol and plays an important role in the alcohol stress response. Therefore, Asr1 is of interest to brewers and winegrowers attempting to improve the techniques of alcoholic fermentation. We verified the importance of Asr1 in the alcohol stress response during alcoholic fermentation. Although we reconfirmed the alcohol-responsive changes in the intracellular localization of Asr1, we could not detect the effects of Asr1-deficiency on Japanese sake brewing or winemaking. In addition, we could not reconfirm the hypersensitivity of Asr1-deficient mutants to alcohol and sodium dodecyl sulfate. Instead, we conclude that Asr1 is not required and nor important for tolerance to alcohol stress.

SYM1 is the stress-induced Saccharomyces cerevisiae ortholog of the mammalian kidney disease gene Mpv17 and is required for ethanol metabolism and tolerance during heat shock

Organisms rapidly adapt to severe environmental stress by inducing the expression of a wide array of heat shock proteins as part of a larger cellular response program. We have used a genomics approach to identify novel heat shock-induced genes in Saccharomyces cerevisiae. The uncharacterized open reading frame (ORF) YLR251W was found to be required for both metabolism and tolerance of ethanol during heat shock. YLR251W has significant homology to the mammalian peroxisomal membrane protein Mpv17, and Mpv17(-/-) mice exhibit age-onset glomerulosclerosis, deafness, hypertension, and, ultimately, death by renal failure. Expression of Mpv17 in ylr251wdelta cells complements the 37 degrees C ethanol growth defect, suggesting that these proteins are functional orthologs. We have therefore renamed ORF YLR251W as SYM1 (for "stress-inducible yeast Mpv17"). In contrast to the peroxisomal localization of Mpv17, we find that Sym1 is an integral membrane protein of the inner mitochondrial membrane. In addition, transcriptional profiling of sym1delta cells uncovered changes in gene expression, including dysregulation of a number of ethanol-repressed genes, exclusively at 37 degrees C relative to wild-type results. Together, these data suggest an important metabolic role for Sym1 in mitochondrial function during heat shock. Furthermore, this study establishes Sym1 as a potential model for understanding the role of Mpv17 in kidney disease and cardiovascular biology.

A Novel Ethanol-Hypersensitive Mutant of Arabidopsis

A novel ethanol-hypersensitive mutant, geko1 (gek1), was isolated from Arabidopsis thaliana. The gek1 mutant displays an enhanced sensitivity (10-100 times greater than the wild type) to ethanol in growth medium, while it grows normally in the absence of ethanol, and responds normally to other alcohols and to environmental stresses such as heat shock and high salinity. The ethanol-hypersensitive phenotype of gek1 requires alcohol dehydrogenase activity, indicating that gek1 is sensitive not to ethanol itself but to the metabolites of ethanol. Consistent with this, gek1 shows enhanced sensitivity to acetaldehyde in the medium. The endogenous acetaldehyde levels were not different between gek1-2 and wild-type seedlings treated with ethanol. These results indicate that the ethanol hypersensitivity of gek1 is due to an enhanced sensitivity to acetaldehyde toxicity, instead of abnormally elevated accumulation of toxic acetaldehyde, which has been thought to be the major cause of ethanol toxicity in mammal cells.

A Novel Arabidopsis Gene Required for Ethanol Tolerance is Conserved Among Plants and Archaea

A novel ethanol-hypersensitive mutant, gek1, of Arabidopsis shows 10-100 times greater sensitivity to ethanol compared to the wild type, while it grows normally in the absence of ethanol, and responds normally to other alcohols and to environmental stresses such as heat shock and high salinity. Mapping of the gek1 locus indicated it is a previously unreported locus. In order to address the GEK1 function, we identified the GEK1 gene by means of map-based cloning. The GEK1 gene encodes a novel protein without any known functional motifs. Transgenic Arabidopsis plants overexpressing GEK1 displayed an enhanced tolerance to ethanol and acetaldehyde, suggesting that GEK1 is directly involved in the tolerance to those chemicals. By contrast, expression of GEK1 in E. coli and yeasts did not increase their tolerance to ethanol or acetaldehyde. Interestingly, a similarity search revealed that GEK1-related genes are conserved only in plants and archaea. These results might suggest that plants, and presumably archaea, have a novel mechanism for protection from acetaldehyde toxicity.

A DMSO-sensitive conditional mutant of the fission yeast orthologue of the Saccharomyces cerevisiae SEC13 gene is defective in septation

Dissection of complex processes using model organisms such as yeasts relies heavily upon the use of conditional mutants. We have generated a collection of fission yeast mutants sensitive to dimethylsulphoxide (DMSO). Among these we have found a mutant in the Schizosaccharomyces pombe orthologue of the Saccharomyces cerevisiae SEC13 gene, which fails to cleave the division septum. Generation of a null allele demonstrates that the S. pombe sec13 gene is essential.

Relationship between lipid composition, frequency of ethanol-induced respiratory deficient mutants, and ethanol tolerance in Saccharomyces cerevisiae

The frequency of ethanol-induced respiratory deficient mutants and lipid composition in two Saccharomyces cerevisiae strains showing different degrees of ethanol tolerance were investigated. The more ethanol-tolerant strain exhibited a lower frequency of ethanol-induced respiratory deficient mutants than the less ethanol-tolerant strain. In addition, the more ethanol-tolerant strain contained a higher ergosterol/phospholipid ratio, a higher proportion of phosphatidylcholine, a lower proportion of phosphatidylethanolamine, a higher incorporation of long-chain fatty acids in total phospholipids, and a slightly higher proportion of unsaturated fatty acids in total phospholipids than the less ethanol-tolerant strain. These results show a clear relationship between the lipid composition, the frequency of ethanol-induced respiratory deficient mutants, and the ethanol tolerance of S. cerevisiae. A possible explanation of this relationship is discussed.

A review of phenotypes in Saccharomyces cerevisiae

A summary of previously defined phenotypes in the yeast Saccharomyces cerevisiae is presented. The purpose of this review is to provide a compendium of phenotypes that can be readily screened to identify pleiotropic phenotypes associated with primary or suppressor mutations. Many of these phenotypes provide a convenient alternative to the primary phenotype for following a gene, or as a marker for cloning a gene by genetic complementation. In many cases a particular phenotype or set of phenotypes can suggest a function for the product of the mutated gene.

The effect of ethanol and specific growth rate on the lipid content and composition of Saccharomyces cerevisiae grown anaerobically in a chemostat

The effects of produced ethanol and specific growth rate on the lipid content and composition of Saccharomyces cerevisiae CBS 2806 were studied using anaerobic chemostat cultures. The cells adapted to increased concentrations of produced ethanol by increasing the proportion of ergosterol at the expense of lanosterol, by increasing the proportion of phosphatidylinositol at the expense of phosphatidylcholine, and by increasing the amount of C18:0 fatty acids in total phospholipids at the expense of C16:0 fatty acids. The produced ethanol had no effect on the phospholipid content nor on the proportion of unsaturated fatty acids in the phospholipids. The specific growth rate had no effect on the phospholipid content, the sterol composition, the phospholipid composition, the fatty acid composition of total phospholipids, or on the proportion of unsaturated fatty acids in the phospholipids of S. cerevisiae. It was not possible to separate the effects of produced ethanol and growth rate on the ergosterol content of the chemostat-grown S. cerevisiae cells.

Ethanol-hypersensitive and ethanol-dependent cdc- mutants in Schizosaccharomyces pombe

Ethanol-hypersensitive strains (ets mutants), unable to grow on media containing 6% ethanol, were isolated from a sample of mutagenized Schizosaccharomyces pombe wild-type cells. Genetic analysis of these ets strains demonstrated that the ets phenotype is associated with mutations in a large set of genes, including cell division cycle (cdc) genes, largely non-overlapping with the set represented by the temperature conditional method; accordingly, we isolated some ets non-ts cdc- mutants, which may identify novel essential genes required for regulation of the S. pombe cell cycle. Conversely, seven well characterized ts cdc- mutants were tested for their ethanol sensitivity; among them, cdc1-7 and cdc13-117 exhibited a tight ets phenotype. Ethanol sensitivity was also tested in strains bearing different alleles of the cdc2 gene, and we found that some of them were ets, but others were non-ets; thus, ethanol hypersensitivity is an allele-specific phenotype. Based on the single base changes found in each particular allele of the cdc2 gene, it is shown that a single amino acid substitution in the p34cdc2 gene product can produce this ets phenotype, and that ethanol hypersensitivity is probably due to the influence of this alcohol on the secondary and/or tertiary structure of the target protein. Ethanol-dependent (etd) mutants were also identified as mutants that can only be propagated on ethanol-containing media. This novel type of conditional phenotype also covers many unrelated genes. One of these etd mutants, etd1-1, was further characterized because of the lethal cdc- phenotype of the mutant cells under restrictive conditions (absence of ethanol). The isolation of extragenic suppressors of etd1-1, and the complementation cloning of a DNA fragment encompassing the etd1+ wild-type gene (or an extragenic multicopy suppressor) demonstrate that current genetic techniques may be applied to mutants isolated by using ethanol as a selective agent.

Regulation of sugar and ethanol metabolism in Saccharomyces cerevisiae

This review briefly surveys the literature on the nature, regulation, genetics, and molecular biology of the major energy-yielding pathways in yeasts, with emphasis on Saccharomyces cerevisiae. While sugar metabolism has received the lion's share of attention from workers in this field because of its bearing on the production of ethanol and other metabolites, more attention is now being paid to ethanol metabolism and the regulation of aerobic metabolism by fermentable and nonfermentable substrates. The utility of yeast as a highly manipulable organism and the discovery that yeast metabolic pathways are subject to the same types of control as those of higher cells open up many opportunities in such diverse areas as molecular evolution and cancer research.

Effect of the chronic ethanol action on the activity of the general amino-acid permease from Saccharomyces cerevisiae var. ellipsoideus

The presence of ethanol and cycloheximide during growth were found to inhibit the function of the general amino-acid permease of Saccharomyces cerevisiae var. ellipsoideus. Contrary to cycloheximide, the effect of ethanol upon growth in alcohol-free medium was reversible. The effect of both inhibitors could be explained in terms of reduction of the number of active carrier molecules located in the plasma membrane.

Ethanol inhibition of Saccharomyces and Candida enzymes

Ethanol inhibition of several hydrolases (sucrase, maltase, trehalase, melezitase and cellobiase) has been measured in both highly ethanol-tolerant Saccharomyces strains (R) and in Candida strains less tolerant to ethanol (S). Cells were either grown in the presence of ethanol and the activities of the enzymes measured without preincubation in this alcohol ("in situ" inhibition assay), or the culture was grown in the absence of ethanol and the activities of the enzymes were determined after preincubation and in the presence of this compound ("in vitro" inhibition assay). Ethanol inhibition (Ki values) of sucrase, maltase, trehalase, and melezitase was quite different for these different enzymes in the same strain (R or S), but similar for the same enzyme in different strains (R and S). The Ki values for cellobiase, which is absent from the R strain, were higher when induced than at the basal level and higher in in vitro assays than in in situ assays. This suggests that the inhibition observed in situ is mainly the result of an inhibition of other proteins related to cellobiase (i.e., those involved in its synthesis) but not a direct inactivation of the enzyme by ethanol. Accordingly, when hybrids between Saccharomyces (R) and Candida (S) strains were constructed by protoplast fusion, and cellobiase was measured in the parental Candida strain and some of the hybrids, there was an increase in the Ki values in the in situ assays from 2.25% ethanol in Candida to 5.5% in some of the hybrids.

Yeast cell viability under conditions of high temperature and ethanol concentrations depends on the mitochondrial genome

Wine yeasts manifest simultaneously a high tolerance to ethanol, thermotolerance, and a high resistance to the mutagenic effects of ethanol on the mitochondrial genome. The transfer of mitochondria from these strains to laboratory yeasts demonstrate that this genome influences the above parameters, since thermotolerance, ethanol-growth tolerance, and the frequency of rho- mutants were either totally or partially modified in the laboratory recipient strain. When the death rate and the rate of formation of rho- mutants were measured under extreme conditions of inhibitory ethanol concentrations and high temperature, a perfect correlation was found between these parameters, and both of them were dependent on the strain of mitochondrial genome. Thus, the transfer of wine yeast mitochondria leads to a lower death rate, and a simultaneous increase in thermotolerance and ethanol tolerance in the recipient strain. These results demonstrate the role that viability plays under conditions of high temperatures and high ethanol concentrations. The greater stability of the rho+ phenotype shown by the wine yeast mitochondrial genome may be responsible for the increased viability conferred by these mitochondria.

Selection of Ethanol-Tolerant Yeast Hybrids in pH-Regulated Continuous Culture

Hybrids between naturally occurring wine yeast strains and laboratory strains were formed as a method of increasing genetic variability to improve the ethanol tolerance of yeast strains. The hybrids were subjected to competition experiments under continuous culture controlled by pH with increasing ethanol concentrations over a wide range to select the fastest-growing strain at any concentration of ethanol. The continuous culture system was obtained by controlling the dilution rate of a chemostat connected to a pH-meter. The nutrient pump of the chemostat was switched on and off in response to the pH of the culture, which was thereby kept near a critical value (pH c ). Under these conditions, when the medium was supplemented with ethanol, the ethanol concentration of the culture increased with each pulse of dilution. A hybrid strain was selected by this procedure that was more tolerant than any of the highly ethanol-tolerant wine yeast strains at any concentration of ethanol and was able to grow at up to 16% (vol/vol) ethanol. This improvement in ethanol tolerance led to an increase in both the ethanol production rate and the total amount of ethanol produced.

Mutations suppressing the effects of a deletion of the phosphoglucose isomerase gene PGI1 in Saccharomyces cerevisiae

A mutant with a deletion covering the phosphoglucose isomerase gene PGI1, allele pgil delta, can only grow on a medium containing fructose and low concentrations of glucose whereas growth is completely inhibited by glucose concentrations higher than 0.4%. This was used to select suppressor mutants restoring growth on synthetic media with 2% glucose as the sole carbon source. One complementation group, SPG1, was defined by recessive mutations. The ability to grow on glucose media was strictly dependent on functional mitochondria. The generation time of the selected mutants on YEP glucose was 6-8 h. No ethanol was formed from glucose and the levels of respiration were very high. These phenotypes were also observed in single pgil delta mutants when growing on fructose media supplemented with 0.4% glucose. The other glycolytic enzymes, the enzymes of the glucose-6-phosphate oxidation pathway as well as catabolite repression were normal in suppressed pgil delta mutants. The suppressor mutation alone caused no abnormal phenotype. The results suggest that the spg1 suppressor mutations allow S. cerevisiae pgil delta mutant strains to grow on glucose by using the Pentose-P cycle in combination with unusual strong respiration.