Possible roles of vacuolar H+-ATPase and mitochondrial function in tolerance to air-drying stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains

Yeasts used in bread making are exposed to air-drying stress during dried yeast production processes. To clarify the genes required for air-drying tolerance, we performed genome-wide screening using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 278 gene deletions responsible for air-drying sensitivity. These genes were classified based on their cellular function and on the localization of their gene products. The results showed that the genes required for air-drying tolerance were frequently involved in mitochondrial functions and in connection with vacuolar H(+)-ATPase, which plays a role in vacuolar acidification. To determine the role of vacuolar acidification in air-drying stress tolerance, we monitored intracellular pH. The results showed that intracellular acidification was induced during air-drying and that this acidification was amplified in a deletion mutant of the VMA2 gene encoding a component of vacuolar H(+)-ATPase, suggesting that vacuolar H(+)-ATPase helps maintain intracellular pH homeostasis, which is affected by air-drying stress. To determine the effects of air-drying stress on mitochondria, we analysed the mitochondrial membrane potential under air-drying stress conditions using MitoTracker. The results showed that mitochondria were extremely sensitive to air-drying stress, suggesting that a mitochondrial function is required for tolerance to air-drying stress. We also analysed the correlation between oxidative-stress sensitivity and air-drying-stress sensitivity. The results suggested that oxidative stress is a critical determinant of sensitivity to air-drying stress, although ROS-scavenging systems are not necessary for air-drying stress tolerance.     

Disruption of six Saccharomyces cerevisiae genes from chromosome IV and basic phenotypic analysis of deletion mutants

We report here the construction of six deletion mutants and the analysis of their basic phenotype. Deletion cassettes containing the KanMX4 marker module and long flanking regions homologous to the target locus were constructed for each of the six open reading-frames (ORFs YDL088c, YDL087c, YDL086w, YDL085w, YDL084w and YDL082w) located on chromosome IV. Sporulation and tetrad analysis of heterozygous deletant strains revealed that, in the FY1679 genetic background, ORFs YDL088c, YDL087c and YDL084w are essential genes for vegetative growth whereas YDL086w, YDL085w and YDL082w are non-essential. ydl088cΔ and ydl084wΔ haploid strains are viable in the CEN. PK2 genetic background although ydl084wΔ grows at a slower rate than the wild type. Complementation tests by corresponding cognate genes confirmed that gene inactivation was responsible for these growth defects. © 1998 John Wiley & Sons, Ltd.     

Systematic analysis of sporulation phenotypes in 624 non-lethal homozygous deletion strains of Saccharomyces cerevisiae

A new high throughput mutant screening procedure for the detection of sporulation mutants was developed and used to analyse a set of 624 non-lethal homozygous deletion mutants created in the European joint research program EUROFAN. The screening procedure involved determination of LL- and DL-dityrosine, sporulation-specific compounds, which were shown to be robust markers of the extent and arrest stage of sporulation mutants. Secondary screens consisted of light microscopy to detect mature and immature spores and DAPI staining to monitor the progress of meiotic nuclear divisions. We discovered new phenotypic classes of mutants defective in spore wall synthesis that were not discovered by previous screens for sporulation mutants. The genes corresponding to the sporulation mutants fell in several functional classes, some of which were previously unknown to be involved in spore formation. Peroxisomes seem to play a role in spore wall synthesis. Mitochondria play a role in sporulation that is not simply restricted to supply of ATP from respiratory metabolism. The deletion mutants included in the set were functionally unknown at the start of EUROFAN; however, within the last few years the importance to sporulation of some of them was also reported by other authors. Taken together, about 8% of all single gene deletion mutants of non-essential genes of Saccharomyces cerevisiae seem to display a clear and reproducible sporulation phenotype.     

Application of the FLP/FRT system for conditional gene deletion in yeast Saccharomyces cerevisiae

The yeast Saccharomyces cerevisiae has proved to be an excellent model organism to study the function of proteins. One of the many advantages of yeast is the many genetic tools available to manipulate gene expression, but there are still limitations. To complement the many methods used to control gene expression in yeast, we have established a conditional gene deletion system by using the FLP/FRT system on yeast vectors to conditionally delete specific yeast genes. Expression of Flp recombinase, which is under the control of the GAL1 promoter, was induced by galactose, which in turn excised FRT sites flanked genes. The efficacy of this system was examined using the FRT site-flanked genes HSP104, URA3 and GFP. The pre-excision frequency of this system, which might be caused by the basal activity of the GAL1 promoter or by spontaneous recombination between FRT sites, was detected ca. 2% under the non-selecting condition. After inducing expression of Flp recombinase, the deletion efficiency achieved ca. 96% of cells in a population within 9 h. After conditional deletion of the specific gene, protein degradation and cell division then diluted out protein that was expressed from this gene prior to its excision. Most importantly, the specific protein to be deleted could be expressed under its own promoter, so that endogenous levels of protein expression were maintained prior to excision by the Flp recombinase. Therefore, this system provides a useful tool for the conditional deletion of genes in yeast.     

Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae

A methodology for large-scale automated phenotypic profiling utilizing quantitative changes in yeast growth has been tested and applied to the analysis of some commonly used laboratory strains. This yeast-adjusted methodology is based on microcultivation in 350 microl liquid medium, where growth is frequently optically recorded, followed by automated extraction of relevant variables from obtained growth curves. We report that cultivation at this micro-scale displayed overall growth features and protein expression pattern highly similar to growth in well aerated medium-scale (10 ml) culture. However, differences were also encountered, mainly relating to the respiratory potential and the production of stress-induced proteins. Quantitative phenotypic profiles for the laboratory yeast strains W303, FY1679 and CEN-PK.2 were screened for in environmental arrays, including 98 different conditions composed of low, medium and high concentrations of 33 growth inhibitors. We introduce the concepts phenotypic index(rate) and phenotypic index(stationary), which relate to changes in rate of growth and the stationary phase optical density increment, respectively, in a particular environment relative a reference strain. The laboratory strains presented selective phenotypic profiles in both phenotypic indexes and the two features appeared in many cases to be independent characteristics. We propose the utilization of this methodology in large-scale screening of the complete collection of yeast deletion mutants.     

Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae

An important recent advance in the functional analysis of Saccharomyces cerevisiae genes is the development of the one-step PCR-mediated technique for deletion and modification of chromosomal genes. This method allows very rapid gene manipulations without requiring plasmid clones of the gene of interest. We describe here a new set of plasmids that serve as templates for the PCR synthesis of fragments that allow a variety of gene modifications. Using as selectable marker the S. cerevisiae TRP1 gene or modules containing the heterologous Schizosaccharomyces pombe his5⁺ or Escherichia coli kan^r gene, these plasmids allow gene deletion, gene overexpression (using the regulatable GAL1 promoter), C- or N-terminal protein tagging [with GFP(S65T), GST, or the 3HA or 13Myc epitope], and partial N- or C-terminal deletions (with or without concomitant protein tagging). Because of the modular nature of the plasmids, they allow efficient and economical use of a small number of PCR primers for a wide variety of gene manipulations. Thus, these plasmids should further facilitate the rapid analysis of gene function in S. cerevisiae. © 1998 John Wiley & Sons, Ltd.     

MSN4基因的过表达对酿酒酵母耐受性的影响研究

以实验室现有菌种AY12a为出发菌株,URA3基因作为筛选标记,利用胞内重组,在MSN4基因的N端加上强启动子PGK1p以实现基因的过表达,最终通过多聚酶链式反应（PCR）验证,成功构建突变株AY12a-msn4。结果表明,该突变株具有一定的耐高温性能,在55 ℃条件下热击后仍能正常生长。同时将突变株AY12a-msn4与出发菌株AY12a进行玉米高温浓醪发酵,并测定发酵完成后的酒精度、残糖、48 h细胞存活率、CO2失重及发酵时间。结果表明,突变株AY12a-msn4发酵液酒精度提高3.85%,48 h细胞存活率上升,残糖含量下降14.5%。     

PCR-mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae

Repeated gene manipulations can be performed in yeast by excision of an introduced marker. Cassette modules containing a marker flanked by two direct repeat sequences of hisG or loxP have often been used for marker recycling, but these leave one copy of the repeats in the chromosome after excision. Genomic copies of a repeat can cause increased mistargeting of constructs containing the same repeats or unexpected chromosomal rearrangements via intra- or interchromosomal recombinations. Here, we describe a novel marker recycling procedure that leaves no scar in the genome, which we have designated seamless gene deletion. A 40 base sequence derived from an adjacent region to the targeted locus was placed in an integrating construct to generate direct repeats after integration. Seamless HIS3 deletion was achieved via a PCR fragment that consisted of a URA3 marker attached to a 40 base repeat-generating sequence flanked by HIS3 targeting sequences at both ends. Transformation of the designed construct resulted in his3 disruption and the generation of 40 base direct repeats on both sides of URA3 in the targeted locus. The resulting his3::URA3 disruptants were plated on 5-fluoroorotic acid medium to select for URA3 loss. All the selected colonies had lost URA3 precisely by recombination between the repeats, resulting in his3 deletion without any extraneous sequences left behind in the chromosome.     

A simple method for isolating disomic strains of Saccharomyces cerevisiae

A simple method to select disomic (N + 1) strains that should be applicable for almost any chromosome in Saccharomyces cerevisiae is presented. A diploid heterozygous for a KanMX knock-out mutation in an essential gene is sporulated and viable geneticin (G418)-resistant colonies selected. Disomic products of a missegregation or non-disjunction event containing a copy of both the wild-type essential gene and its complementary KanMX knock-out allele make up most of the viable colonies. This method has been used to isolate disomic haploids for a variety of chromosomes. It is appropriately named MARV (for missegregation-associated restoration of viability) and is easily adaptable to virtually any strain.     

Computational approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection

Within this study, we have used a set of computational techniques to relate the genotypes and phenotypes of natural populations of Saccharomyces cerevisiae, using allelic information from 11 microsatellite loci and results from 24 phenotypic tests. A group of 103 strains was obtained from a larger S. cerevisiae winemaking strain collection by clustering with self‐organizing maps. These strains were further characterized regarding their allelic combinations for 11 microsatellites and analysed in phenotypic screens that included taxonomic criteria (carbon and nitrogen assimilation tests, growth at different temperatures) and tests with biotechnological relevance (ethanol resistance, H₂S or aromatic precursors formation). Phenotypic variability was rather high and each strain showed a unique phenotypic profile. The results, expressed as optical density (A₆₄₀) after 22 h of growth, were in agreement with taxonomic data, although with some exceptions, since few strains were capable of consuming arabinose and ribose to a small extent. Based on microsatellite allelic information, naïve Bayesian classifier correctly assigned (AUC = 0.81, p < 10^?8) most of the strains to the vineyard from where they were isolated, despite their close location (50–100 km). We also identified subgroups of strains with similar values of a phenotypic feature and microsatellite allelic pattern (AUC > 0.75). Subgroups were found for strains with low ethanol resistance, growth at 30 °C and growth in media containing galactose, raffinose or urea. The results demonstrate that computational approaches can be used to establish genotype–phenotype relations and to make predictions about a strain's biotechnological potential. Copyright © 2009 John Wiley & Sons, Ltd.     

乙酰辅酶A含量对酿酒酵母乙酸乙酯合成的影响

通过缺失乙酰辅酶A水解酶（ACH）基因和过表达乙酰辅酶A合成酶（ACS）基因技术提高酿酒酵母合成乙酰辅酶A（acetyl- CoA）能力的同时,过表达醇酰基转移酶（ATF）基因,提高乙酸乙酯合成能力,并考察acetyl-CoA含量对酿酒酵母合成乙酸乙酯能力的影响。结果表明,敲除ACH1基因、且在敲除ACH1基因基础上过表达ACS1、ACS2基因均能提高酿酒酵母Acetyl-CoA含量,进而提高乙酸乙酯含量。较亲本菌株α5,缺失突变株α5ΔACH1、重组菌株α5-A1、α5-A2的Acetyl-CoA的含量均分别提高了52.5%、80.33%、52.79%,乙酸乙酯含量分别提高10.59%、26.12%、23.70%。在敲除ACH1基因、过表达ACS1和ACS2基因的基础上同时过表达ATF1基因,得到工程菌株A1-ATF1和A2-ATF1,较亲本菌株α5,乙酸乙酯含量分别提高226.09%、530.43%、289.57%,工程菌株A1-ATF1乙酸乙酯产量最高,为72.52 mg/L。研究表明,提高乙酰辅酶A含量能够促进乙酸乙酯的合成,为提高乙酸乙酯生成量提供了新思路。     

Designer deletion and prototrophic strains derived from Saccharomyces cerevisiae strain W303‐1a

We report the construction of Saccharomyces cerevisiae strains isogenic to W303‐1a that are designed to allow efficient genetic analysis. To facilitate the generation of null alleles of target genes by PCR‐mediated gene disruption, we constructed designer deletion alleles of the ARG4, TRP1 and URA3 genes. In addition, a single pair of oligonucleotide primers were designed that can be used to amplify any of several marker genes for use in PCR‐mediated gene disruption. A new version of the ‘reusable’ hisG‐URA3‐hisG cassette was constructed for use in PCR‐mediated gene disruption. Finally, to facilitate the formation of isogenic diploids by selection, we constructed strains that contain combinations of wild‐type alleles of ADE2, HIS3, LEU2, TRP1 and URA3. Copyright © 1999 John Wiley & Sons, Ltd.     

Additional vectors for PCR-based gene tagging in Saccharomyces cerevisiae and Schizosaccharomyces pombe using nourseothricin resistance

The one-step PCR-mediated technique used for modification of chromosomal loci is a powerful tool for functional analysis in yeast. Both Saccharomyces cerevisiae and Schizosaccharomyces pombe are amenable to this technique. However, the scarce availability of selectable markers for Sz. pombe hampers the easy use of this technique in this species. Here, we describe the construction of new vectors deriving from the pFA6a family, which are suitable for tagging in both yeasts owing to the presence of a nourseothricin-resistance cassette. These plasmids allow various gene manipulations at chromosomal loci, viz. N- and C-terminal tagging with 3HA (haemagglutinin) or 13Myc epitopes, GST (glutathione S-transferase), 4TAP (tandem affinity purification) and several GFP (green fluorescent protein) isoforms. For N-terminal modifications, the use of different promoters allows constitutive (PADH1) or regulatable (PGAL1) promoters for S. cerevisiae and derivatives of Pnmt1 for Sz. pombe expression.     

Efficient PCR-based gene disruption in Saccharomyces strains using intergenic primers

Gene disruptions are a vital tool for understanding Saccharomyces cerevisiae gene function. An arrayed library of gene disruption strains has been produced by a consortium of yeast laboratories; however their use is limited to a single genetic background. Since the yeast research community works with several different strain backgrounds, disruption libraries in other common laboratory strains are desirable. We have developed simple PCR-based methods that allow transfer of gene disruptions from the S288C-derived strain library into any Saccharomyces strain. One method transfers the unique sequence tags that flank each of the disrupted genes and replaces the kanamycin resistance marker with a recyclable URA3 gene from Kluyveromyces lactis. All gene-specific PCR amplifications for this method are performed using a pre-existing set of primers that are commercially available. We have also extended this PCR technique to develop a second general gene disruption method suitable for any transformable strain of Saccharomyces.     

Diacetyl reduction by commercial Saccharomyces cerevisiae strains during vinification

Microbially derived diacetyl accumulation during vinification imparts a buttery wine aroma, which has stylistic implications. However, at higher concentrations diacetyl induces an aromatic off‐flavour. Saccharomyces cerevisiae is able to reduce diacetyl to below the sensory threshold. Therefore, characterization of the diacetyl reduction in commercial wine yeasts creates new opportunities to manage the risk of wine associated off‐flavours. Diacetyl reduction by two commercial S. cerevisiae strains was characterized in Pinot blanc grape must of the vintage 2012 with different initial diacetyl concentrations (0–50 mg/L). Highest diacetyl reduction was found in the first two days after wine yeasts were inoculated. No further decrease in diacetyl content was observed after the fourth day. All assays in which diacetyl was added showed the same final diacetyl concentration of approximately 2 mg/L. However, a significantly lower amount of diacetyl was found in grape must without adding diacetyl. The present results indicate that commercial wine yeasts are able to reduce much higher amounts of diacetyl than normally expected during the vinification procedure. However, the constant final diacetyl concentration indicates that diacetyl accumulation may be the result of wine matrix binding effects, which prevent a complete reduction by active wine yeasts. Copyright © 2013 The Institute of Brewing & Distilling.     

Genetic and enological analysis of selected Saccharomyces cerevisiae strains for wine production

The non‐wine Saccharomyces cerevisiae strain of 96581 was found to be a promising candidate for the production of white wine. It produced wines with fusel alcohols that were 57% higher than those produced by the wine yeasts studied and was also more efficient in the production of 2‐phenethyl acetate and 3‐methyl‐1‐butanol acetate. This study also shows that there is a difference in the ester‐formation efficiency for acetates relative to C6, C8 and C10 fatty acid esters for all the studied yeast strains. Therefore, it supports the view that other unidentified enzymes besides those regulated by ATF1 and ATF2 genes are involved in the production of ethyl esters of C6–C10 fatty acids. DNA analysis of the 25S, 18S, 5.8S and 5S ribosomal DNA genes in these strains showed high conservation. Despite the closely related nature of these yeast strains, the chemical profiles of the wines produced were significantly different.     

常压室温等离子体诱变选育耐酸酿酒酵母菌株

利用常压室温等离子体(ARTP)诱变方法对实验室保藏的酿酒酵母(Saccharomyces cerevisiae)SC-62进行诱变,通过试验确定最佳诱变条件为处理时长80 s,此条件下菌株SC-62致死率84%。将诱变获得的菌株进行初筛、复筛和发酵性能测定。结果显示,筛选出一株耐酸性强、发酵性能优良的正突变菌株A-107,其在pH为2.5的发酵培养基上培养6 d后测得的发酵力[6.21 g CO2/(100 mL·24 h)]和酒精产量(11.52%vol)较出发菌株SC-62分别提高了37%和30%,突变菌株A-107可耐受16%乙醇、100 g/L NaCl、500 g/L葡萄糖,耐受性和遗传稳定性良好。     

常压室温等离子体诱变选育耐酸酿酒酵母菌株

利用常压室温等离子体(ARTP)诱变方法对实验室保藏的酿酒酵母(Saccharomyces cerevisiae)SC-62进行诱变,通过试验确定最佳诱变条件为处理时长80 s,此条件下菌株SC-62致死率84%。将诱变获得的菌株进行初筛、复筛和发酵性能测定。结果显示,筛选出一株耐酸性强、发酵性能优良的正突变菌株A-107,其在pH为2.5的发酵培养基上培养6 d后测得的发酵力[6.21 g CO2/(100 mL·24 h)]和酒精产量(11.52%vol)较出发菌株SC-62分别提高了37%和30%,突变菌株A-107可耐受16%乙醇、100 g/L NaCl、500 g/L葡萄糖,耐受性和遗传稳定性良好。     

The chromosomal constitution of wine strains of Saccharomyces cerevisiae

A general procedure is described for determining the chromosomal constitution of industrial strains of Saccharomyces cerevisiae based on analysis of segregation frequencies for input markers among random spore progeny of industrial-laboratory strain hybrids. The multiply auxotrophic haploid testers used carried a dominant erythromycin-resistance marker, allowing hybrids to be selected in mass matings with spores produced by the wild-type industrial strains. Analysis of a number of independent crosses between the haploid testers and an unselected population of spores of each wine strain distinguished between disomic, trisomic and tetrasomic chromosomal complements in the parents. Possible explanations for a significant class of aberrant segregation frequencies are discussed. Results of the analysis indicate that UCD Enology 522 (Montrachet) is diploid and possibly trisomic for chromosome VII; 522X is diploid; UCD Enology 505 (California Champagne) is disomic for chromosome XVI, trisomic for chromosomes I, II, III, VI, VIII, IX, X, XII, XV, tetrasomic for chromosomes IV, XI, XIII, XIV and either trisomic or tetrasomic for chromosomes V and VII; and that UCD Enology 595 (Pasteur Champagne) is disomic for chromosomes I, II, III, IX, XVI, trisomic for chromosomes IV, VI, X, XII, XIV, XV, tetrasomic for chromosomes V, VIII, XI, XIII and either disomic or tetrasomic for chromosome VII.     

基于代谢组学方法的两株酿酒酵母菌胞内差异代谢产物分析

为了解不同发酵时期的酿酒酵母菌的胞内小分子化合物的代谢状况,该研究应用代谢组学方法,分析了重组酵母菌株N6076及其原始菌株Kh08的胞内差异代谢产物。UPLC-Q-TOF/MS的检测分析结果表明,2株酵母菌不同发酵时间点的胞内小分子代谢产物存在差异,其种类分别为11和10种,且以高丰度的脂类物质居多,其中甲羟戊酸-5-磷酸和胱氨酸分别为2株酵母菌胞内的显著差异代谢产物。应用LC-MS/MS对甲羟戊酸代谢途径中甲羟戊酸-5-磷酸(MVAP)的检测分析结果表明,重组菌株N6076发酵48 h时胞内MVAP浓度为1. 32μg/mL,而原始菌株Kh08在相同发酵时间点未检出MVAP。该研究为进一步认识酵母菌胞内小分子化合物的代谢提供了依据。