A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study.

Genomics, transcriptomics, proteomics and fluxomics are powerful omics-technologies that play a major role in today's research. For each of these techniques good sample quality is crucial. Major factors contributing to the quality of a sample is the actual sampling procedure itself and the way the sample is stored directly after sampling. It has already been described that RNAlater can be used to store tissues and cells in a way that the RNA quality and quantity are preserved. In this paper, we demonstrate that quaternary ammonium salts (RNAlater) are also suitable to preserve and store samples from Saccharomyces cerevisiae for later use with the four major omics-technologies. Moreover, it is shown that RNAlater also preserves the cell morphology and the potential to recover growth, permitting microscopic analysis and yeast cell culturing at a later stage.

Contribution of monophenols to beer flavour based on flavour thresholds, interactions and recombination experiments.

Although monophenols are known to contribute to the flavour of many foods and beverages, little is known about their influence on beer flavour. Therefore, the contribution of 11 monophenols to the overall beer flavour was studied by determining their flavour thresholds. Large differences in sensitivity were observed between individual tasters. Next, flavour interactions between monophenols were examined in nine binary mixtures, which showed that strong interactions like synergy and antagonism occur. Based on these results, the flavour contribution of the monophenols was estimated by calculating flavour units. These proved to be rather low for most of the studied monophenols. However, recombination experiments demonstrated that monophenols enriched beer flavour with spicy, smokey and vanilla flavour aspects. This showed how monophenols might influence overall flavour, even at sub-threshold concentrations.

Flocculation gene variability in industrial brewer's yeast strains.

The brewer's yeast genome encodes a 'Flo' flocculin family responsible for flocculation. Controlled floc formation or flocculation at the end of fermentation is of great importance in the brewing industry since it is a cost-effective and environmental-friendly technique to separate yeast cells from the final beer. FLO genes have the notable capacity to evolve and diverge many times faster than other genes. In actual practice, this genetic variability may directly alter the flocculin structure, which in turn may affect the flocculation onset and/or strength in an uncontrolled manner. Here, 16 ale and lager yeast strains from different breweries, one laboratory Saccharomyces cerevisiae and one reference Saccharomyces pastorianus strain, with divergent flocculation strengths, were selected and screened for characteristic FLO gene sequences. Most of the strains could be distinguished by a typical pattern of these FLO gene markers. The FLO1 and FLO10 markers were only present in five out of the 18 yeast strains, while the FLO9 marker was ubiquitous in all the tested strains. Surprisingly, three strongly flocculating ale yeast strains in this screening also share a typical 'lager' yeast FLO gene marker. Further analysis revealed that a complete Lg-FLO1 allele was present in these ale yeasts. Taken together, this explicit genetic variation between flocculation genes hampers attempts to understand and control the flocculation behavior in industrial brewer's yeasts.

The influence of yeast oxygenation prior to brewery fermentation on yeast metabolism and the oxidative stress response.

Yeast preoxygenation can confer important advantages to brewery fermentations by means of omitting the need to oxygenate the wort. However, the impact of yeast preoxygenation on yeast metabolism has never been assessed systematically. Therefore, expression analysis was performed of genes that are of importance in oxygen-dependent pathways, oxidative stress response and general stress response during 8 h of preoxygenation. The gene expressions of both the important transcription factors Hap1 and Rox1, involved in oxygen sensing, were mainly increased in the first 3 h, while YAP1 expression, which is involved in the oxidative stress response, increased drastically only in the first 45 min. The results also show that stress-responsive genes (HSP12, SSA3, PAU5, SOD1, SOD2, CTA1 and CTT1) were induced during the process, together with the accumulation of trehalose. The accumulation of ergosterol and unsaturated fatty acids was accompanied by the expression of ERG1, ERG11 and OLE1. Genes involved in respiration (QCR9, COX15, CYC1 and CYC7) also increased during preoxygenation. Yeast viability did not decrease during the process, and the fermentation performance of the yeast reached a maximum after 5 h of preoxygenation. These results suggest that yeast cells acquire a stress response along the preoxygenation period, which makes them more resistant against the stressful conditions of the preoxygenation process and the subsequent fermentation.

Phenotypic diversity of Flo protein family-mediated adhesion in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae genome encodes a Flo (flocculin) adhesin family responsible for cell-cell and cell-surface adherence. In commonly used laboratory strains, these FLO genes are transcriptionally silent, because of a nonsense mutation in the transcriptional activator FLO8, concealing the potential phenotypic diversity of fungal adhesion. Here, we analyse the distinct adhesion characteristics conferred by each of the five FLO genes in the S288C strain and compare these phenotypes with a strain containing a functional copy of FLO8. Our results show that four FLO genes confer flocculation, but with divergent characteristics such as binding strength, carbohydrate recognition and floc size. Adhesion to agar surfaces, on the other hand, largely depended on two adhesins, Flo10 and Flo11. Expression of any FLO gene caused a significant increase in cell wall hydrophobicity. Nevertheless, the capacity to adhere to plastic surfaces, which is believed to depend on hydrophobic interactions, differed strongly between the adhesins. Restoring Flo8 yielded both flocculation and cell-surface adherence, such as invasive growth, a phenotype not observed when any of the single FLO genes was overexpressed. Taken together, this study reveals how S. cerevisiae carries a small reservoir of FLO genes that allows cells to display a wide variety of adhesive properties.

Stability of high cell density brewery fermentations during serial repitching.

The volumetric productivity of the beer fermentation process can be increased by using a higher pitching rate (i.e. higher inoculum size). However, the decreased yeast net growth observed in these high cell density brewery fermentations can adversely affect the physiological stability throughout subsequent yeast generations. Therefore, different O(2) conditions (wort aeration and yeast preoxygenation) were applied to high cell density fermentation and eight generations of fermentations were evaluated together with conventional fermentations. Freshly propagated high cell density populations adapted faster to the fermentative conditions than normal cell density populations. Preoxygenating the yeast was essential for the yeast physiological and beer flavor compound stability of high cell density fermentations during serial repitching. In contrast, the use of non-preoxygenated yeast resulted in inadequate growth which caused (1) insufficient yield of biomass to repitch all eight generations, (2) a 10% decrease in viability, (3) a moderate increase of yeast age, (4) and a dramatic increase of the unwanted flavor compounds acetaldehyde and total diacetyl during the sequence of fermentations. Therefore, to achieve sustainable high cell density fermentations throughout the economical valuable process of serial repitching, adequate yeast growth is essential.

Optimisation of a complete method for the analysis of volatiles involved in the flavour stability of beer by solid-phase microextraction in combination with gas chromatography and mass spectrometry.

Headspace solid-phase microextraction combined with gas chromatography and mass spectrometry was used for the quantification of 32 volatiles which represent the typical chemical reactions that can occur during beer ageing. Detection was accomplished by employing on-fibre derivatisation using o-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine (PFBHA) and normal HS-SPME extraction. The procedures were optimised for SPME fibre selection, PFBHA loading temperature and time, extraction temperature and time, and effect of salt addition. Interference of matrix effects was overcome by calibrating according to the standard addition method and by using internal standards. Afterwards, the method was validated successfully and was applied to study the flavour stability of different beer types.

Optimisation of wort volatile analysis by headspace solid-phase microextraction in combination with gas chromatography and mass spectrometry.

The aim of this study was to create a simple, solventless technique without derivatisation in order to analyze a broad range of volatiles in beer wort. A method was developed using headspace solid-phase microextraction coupled with gas chromatography and mass spectrometry. The procedure was optimised by selection of the appropriate fibre and optimisation of extraction temperature, extraction time, and salting-out. The detection limits were well below the actual wort concentrations of the selected volatiles, ranging from 12 ng/l for linalool to 0.53 microg/l for furfural. Moreover, the procedure showed a good linearity and was applied to the analysis of wort samples taken from a wort boiling process in an industrial brewery.

Characterization of volatiles in unhopped wort.

The volatile fraction of wort components was studied during boiling. Not less than 118 volatile compounds were identified when unhopped pilsner wort was boiled and samples of wort and condensed vapors were analyzed with headspace SPME-GC/MS, of which 54 were confirmed with reference compounds. The wort samples contained 61 identifiable compounds, while the vapor condensate yielded 108 different compounds. Almost 30 known compounds were found that have not been described before in unhopped pilsner wort. One previously unknown aldol reaction product was tentatively identified as 2-phenyl-2-octenal. The detection of branched 2-alkenals underlines the importance of the aldol condensation in Maillard-type reactions, while the tentative identification of alkyloxazoles and alkylthiazoles could once more accentuate the central role of alpha-dicarbonyl compounds, aldehydes, and amino acids in flavor generation. The condensation of wort vapors joined with the SPME-GC/MS technique has proven to be a useful tool in volatile analysis.

Influence of lipids in the generation of phenylacetaldehyde in wort-related model systems.

The effect of lipids on the formation of the Strecker aldehyde phenylacetaldehyde during wort boiling was studied to determine the role that small changes in the lipid content of the wort have in the production of significant flavor compounds in beer. Wort was treated with 0-2.77 mmol per liter of glucose, linoleic acid, or 2,4-decadienal and heated at 60-98 degrees C for 1 h. After this time, the amount of the Strecker aldehyde phenylacetaldehyde increased in the samples treated with linoleic acid or decadienal but not in the samples treated with glucose. Thus, the amount of phenylacetaldehyde produced in the presence of linoleic acid was 1.1-2.5 times the amount of the Strecker aldehyde produced in the control wort, and this amount increased to 3.6-4.6 times when decadienal was employed. The higher reactivity of decadienal than linoleic acid for this reaction decreased with temperature and was related to the oxidation of linoleic acid that occurred to a higher extent at higher temperatures. The above results suggest that lipids can contribute to the formation of Strecker aldehydes during wort boiling and that changes in the lipid content of the wort will produce significant changes in the formation of Strecker aldehydes in addition to other well-known consequences in beer quality and yeast metabolism. On the other hand, because of the high glucose content in wort, small changes in its content are not expected to affect the amount of Strecker aldehydes produced.

Variability in the release of free and bound hydroxycinnamic acids from diverse malted barley (Hordeum vulgare L.) cultivars during wort production.

Volatile phenols have long been recognized as important flavor contributors to the aroma of various alcoholic beverages. The two main flavor-active volatile phenols in beer are 4-vinylguaiacol and 4-vinylphenol. They are the decarboxylation products of the precursors ferulic acid and p-coumaric acid, respectively, which are released during the brewing process, mainly from malt. In this study, the variability in the release of free and ester-bound hydroxycinnamic acids from nine malted barley ( Hordeum vulgare L.) varieties during wort production was investigated. A large variability between different barley malts and their corresponding worts was observed. Differences were also found between free ferulic acid levels from identical malt varieties originating from different malt houses. During mashing, free hydroxycinnamic acids in wort are both water-extracted and enzymatically released by cinnamoyl esterase activity. Esterase activities clearly differ between different barley malt varieties. Multiple linear regression analysis showed that the release of ferulic acid during mashing did not depend only on the barley malt esterase activity but also on the amount of ester-bound ferulic acid initially present in the wort and on its endoxylanase activity. The study demonstrates the importance of selecting a suitable malt variety as the first means of controlling the final volatile phenol levels in beer.

Determination of hydroxycinnamic acids and volatile phenols in wort and beer by isocratic high-performance liquid chromatography using electrochemical detection.

The suitability of a simple and rapid isocratic RP-HPLC method with amperometric electrochemical detection for the simultaneous detection and quantification of hydroxycinnamic acids and their corresponding aroma-active volatile phenols in wort and beer is reported. The technique gives good specificity and sensitivity, and can therefore be used for routine monitoring of hydroxycinnamic acids in wort and the development of volatile phenolic flavour compounds during the beer production process and subsequent conservation.

Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival.

UNLABELLED: We studied the flocculation mechanism at the molecular level by determining the atomic structures of N-Flo1p and N-Lg-Flo1p in complex with their ligands. We show that they have similar ligand binding mechanisms but distinct carbohydrate specificities and affinities, which are determined by the compactness of the binding site. We characterized the glycans of Flo1p and their role in this binding process and demonstrate that glycan-glycan interactions significantly contribute to the cell-cell adhesion mechanism. Therefore, the extended flocculation mechanism is based on the self-interaction of Flo proteins and this interaction is established in two stages, involving both glycan-glycan and protein-glycan interactions. The crucial role of calcium in both types of interaction was demonstrated: Ca(2+) takes part in the binding of the carbohydrate to the protein, and the glycans aggregate only in the presence of Ca(2+). These results unify the generally accepted lectin hypothesis with the historically first-proposed "Ca(2+)-bridge" hypothesis. Additionally, a new role of cell flocculation is demonstrated; i.e., flocculation is linked to cell conjugation and mating, and survival chances consequently increase significantly by spore formation and by introduction of genetic variability. The role of Flo1p in mating was demonstrated by showing that mating efficiency is increased when cells flocculate and by differential transcriptome analysis of flocculating versus nonflocculating cells in a low-shear environment (microgravity). The results show that a multicellular clump (floc) provides a uniquely organized multicellular ultrastructure that provides a suitable microenvironment to induce and perform cell conjugation and mating. IMPORTANCE: Yeast cells can form multicellular clumps under adverse growth conditions that protect cells from harsh environmental stresses. The floc formation is based on the self-interaction of Flo proteins via an N-terminal PA14 lectin domain. We have focused on the flocculation mechanism and its role. We found that carbohydrate specificity and affinity are determined by the accessibility of the binding site of the Flo proteins where the external loops in the ligand-binding domains are involved in glycan recognition specificity. We demonstrated that, in addition to the Flo lectin-glycan interaction, glycan-glycan interactions also contribute significantly to cell-cell recognition and interaction. Additionally, we show that flocculation provides a uniquely organized multicellular ultrastructure that is suitable to induce and accomplish cell mating. Therefore, flocculation is an important mechanism to enhance long-term yeast survival.

Glucose and sucrose: hazardous fast-food for industrial yeast?

Yeast cells often encounter a mixture of different carbohydrates in industrial processes. However, glucose and sucrose are always consumed first. The presence of these sugars causes repression of gluconeogenesis, the glyoxylate cycle, respiration and the uptake of less-preferred carbohydrates. Glucose and sucrose also trigger unexpected, hormone-like effects, including the activation of cellular growth, the mobilization of storage compounds and the diminution of cellular stress resistance. In an industrial context, these effects lead to several yeast-related problems, such as slow or incomplete fermentation, 'off flavors' and poor maintenance of yeast vitality. Recent studies indicate that the use of mutants with altered responses to carbohydrates can significantly increase productivity. Alternatively, avoiding unnecessary exposure to glucose and sucrose could also improve the performance of industrial yeasts.

Ferulic acid release and 4-vinylguaiacol formation during brewing and fermentation: indications for feruloyl esterase activity in Saccharomyces cerevisiae.

The release of ferulic acid and the subsequent thermal or enzymatic decarboxylation to 4-vinylguaiacol are inherent to the beer production process. Phenolic, medicinal, or clove-like flavors originating from 4-vinylguaiacol frequently occur in beer made with wheat or wheat malt. To evaluate the release of ferulic acid and the transformation to 4-vinylguaiacol, beer was brewed with different proportions of barley malt, wheat, and wheat malt. Ferulic acid as well as 4-vinylguaiacol levels were determined by HPLC at several stages of the beer production process. During brewing, ferulic acid was released at the initial mashing phase, whereas moderate levels of 4-vinylguaiacol were formed by wort boiling. Higher levels of the phenolic flavor compound were produced during fermentations with brewery yeast strains of the Pof(+) phenotype. In beer made with barley malt, ferulic acid was mainly released during the brewing process. Conversely, 60-90% of ferulic acid in wheat or wheat malt beer was hydrolyzed during fermentation, causing higher 4-vinylguaiacol levels in these beers. As cereal enzymes are most likely inactivated during wort boiling, the additional release of ferulic acid during fermentation suggests the activity of feruloyl esterases produced by brewer's yeast.

Influence of the brewing process on furfuryl ethyl ether formation during beer aging.

In beer, the development of a solvent-like stale flavor is associated with the formation of furfuryl ethyl ether. The synthesis rate of this important flavor compound is proportional to the concentration of furfuryl alcohol in beer. This study shows that furfuryl alcohol in beer is mainly formed by Maillard reactions initiated during wort boiling and malt production. A mechanism for its formation from alpha-(1,4)-oligoglucans and amino acids in wort and beer is proposed. During wort boiling, a quadratic relationship was found between the wort extract concentration, on the one hand, and the increase of furfuryl alcohol and furfural, on the other. The reduction of furfural by yeast during fermentation further increases the furfuryl alcohol content. In pale beers, the furfuryl alcohol concentration is essentially determined by the thermal load on wort during brewing operations. In dark beers, a considerable fraction of furfuryl alcohol may, however, come from the dark malts used. These results lead to important practical conclusions concerning the control over furfuryl ethyl ether in beer.

Flavor-active esters: adding fruitiness to beer.

As they are responsible for the fruity character of fermented beverages, volatile esters constitute an important group of aromatic compounds in beer. In modern high-gravity fermentations, which are performed in tall cylindroconical vessels, the beer ester balance is often sub-optimal, resulting in a clear decrease in beer quality. Despite the intensive research aimed at unravelling the precise mechanism and regulation of ester synthesis, our current knowledge remains far from complete. However, a number of factors that influence flavor-active ester production have already been described, including wort composition, wort aeration and fermentor design. A thoughtful adaptation of these parameters allows brewers to steer ester concentrations and thus to control the fruity character of their beers. This paper reviews the current knowledge of the biochemistry behind yeast ester synthesis and discusses the different factors that allow ester formation to be controlled during brewery fermentation.

The influence of microgravity on invasive growth in Saccharomyces cerevisiae.

This study investigates the effects of microgravity on colony growth and the morphological transition from single cells to short invasive filaments in the model eukaryotic organism Saccharomyces cerevisiae. Two-dimensional spreading of the yeast colonies grown on semi-solid agar medium was reduced under microgravity in the Σ1278b laboratory strain but not in the CMBSESA1 industrial strain. This was supported by the Σ1278b proteome map under microgravity conditions, which revealed upregulation of proteins linked to anaerobic conditions. The Σ1278b strain showed a reduced invasive growth in the center of the yeast colony. Bud scar distribution was slightly affected, with a switch toward more random budding. Together, microgravity conditions disturb spatially programmed budding patterns and generate strain-dependent growth differences in yeast colonies on semi-solid medium.

Determination of volatile monophenols in beer using acetylation and headspace solid-phase microextraction in combination with gas chromatography and mass spectrometry.

Monophenols are widely spread compounds contributing to the flavour of many foods and beverages. They are most likely present in beer, but so far, little is known about their influence on beer flavour. To quantify these monophenols in beer, we optimised a headspace solid-phase microextraction method coupled to gas chromatography-mass spectrometry. To improve their isolation from the beer matrix and their chromatographic properties, the monophenols were acetylated using acetic anhydride and KHCO(3) as derivatising agent and base catalyst, respectively. Derivatisation conditions were optimised with attention for the pH of the reaction medium. Additionally, different parameters affecting extraction efficiency were optimised, including fibre coating, extraction time and temperature and salt addition. Afterwards, we calibrated and validated the method successfully and applied it for the analysis of monophenols in beer samples.

Production and biological function of volatile esters in Saccharomyces cerevisiae.

The need to understand and control ester synthesis is driven by the fact that esters play a key role in the sensorial quality of fermented alcoholic beverages like beer, wine and sake. As esters are synthesized in yeast via several complex metabolic pathways, there is a need to gain a clear understanding of ester metabolism and its regulation. The individual genes involved, their functions and regulatory mechanisms have to be identified. In alcoholic beverages, there are two important groups of esters: the acetate esters and the medium-chain fatty acid (MCFA) ethyl esters. For acetate ester synthesis, the genes involved have already been cloned and characterized. Also the biochemical pathways and the regulation of acetate ester synthesis are well defined. With respect to the molecular basis of MCFA ethyl ester synthesis, however, significant progress has only recently been made. Next to the characterization of the biochemical pathways and regulation of ester synthesis, a new and more important question arises: what is the advantage for yeast to produce these esters? Several hypotheses have been proposed in the past, but none was satisfactorily. This paper reviews the current hypotheses of ester synthesis in yeast in relation to the complex regulation of the alcohol acetyl transferases and the different factors that allow ester formation to be controlled during fermentation.