Genetic analysis of the metabolic pathways responsible for aroma metabolite production by Saccharomyces cerevisiae

Exploring jujube wine flavor and fermentation mechanisms by HS-SPME-GC-MS and UHPLC-MS metabolomics

The fermentation metabolites significantly influence the quality of jujube wine. However, the dynamics of these metabolites during fermentation are not well understood. In this study, a total of 107 volatile and 1758 non-volatile compounds were identified using a flavor-directed research strategy and non-targeted metabolomics. The increase in esters and alcohols during fermentation shifted the aroma from grassy, mushroomy, and earthy to a floral and fruity flavor in the jujube wine. Leucine and phenylalanine were notably enriched during fermentation, potentially benefiting human health and enriching the flavor of fruit wines. Moreover, pathway analysis identified four key metabolic pathways and two crucial metabolic substrates, pyruvate and l-aspartate. This study provides a theoretical reference for optimizing the fermentation process and enhancing the quality of jujube wine.

The origins of the Guinness stout yeast

Beer is made via the fermentation of an aqueous extract predominantly composed of malted barley flavoured with hops. The transforming microorganism is typically a single strain of Saccharomyces cerevisiae, and for the majority of major beer brands the yeast strain is a unique component. The present yeast used to make Guinness stout brewed in Dublin, Ireland, can be traced back to 1903, but its origins are unknown. To that end, we used Illumina and Nanopore sequencing to generate whole-genome sequencing data for a total of 22 S. cerevisiae yeast strains: 16 from the Guinness collection and 6 other historical Irish brewing. The origins of the Guinness yeast were determined with a SNP-based analysis, demonstrating that the Guinness strains occupy a distinct group separate from other historical Irish brewing yeasts. Assessment of chromosome number, copy number variation and phenotypic evaluation of key brewing attributes established Guinness yeast-specific SNPs but no specific chromosomal amplifications. Our analysis also demonstrated the effects of yeast storage on phylogeny. Altogether, our results suggest that the Guinness yeast used today is related to the first deposited Guinness yeast; the 1903 Watling Laboratory Guinness yeast.

Improvement of Fusel Alcohol Production by Engineering of the Yeast Branched-Chain Amino Acid Aminotransaminase

Branched-chain higher alcohols (BCHAs), or fusel alcohols, including isobutanol, isoamyl alcohol, and active amyl alcohol, are useful compounds in several industries. The yeast Saccharomyces cerevisiae can synthesize these compounds via the metabolic pathways of branched-chain amino acids (BCAAs). Branched-chain amino acid aminotransaminases (BCATs) are the key enzymes for BCHA production via the Ehrlich pathway of BCAAs. BCATs catalyze a bidirectional transamination reaction between branched-chain α-keto acids (BCKAs) and BCAAs. In S. cerevisiae, there are two BCAT isoforms, Bat1 and Bat2, which are encoded by the genes BAT1 and BAT2. Although many studies have shown the effects of deletion or overexpression of BAT1 and BAT2 on BCHA production, there have been no reports on the enhancement of BCHA production by functional variants of BCATs. Here, to improve BCHA productivity, we designed variants of Bat1 and Bat2 with altered enzyme activity by using in silico computational analysis: the Gly333Ser and Gly333Trp Bat1 and corresponding Gly316Ser and Gly316Trp Bat2 variants, respectively. When expressed in S. cerevisiae cells, most of these variants caused a growth defect in minimal medium. Interestingly, the Gly333Trp Bat1 and Gly316Ser Bat2 variants achieved 18.7-fold and 17.4-fold increases in isobutanol above that for the wild-type enzyme, respectively. The enzyme assay revealed that the catalytic activities of all four BCAT variants were lower than that of the wild-type enzyme. Our results indicate that the decreased BCAT activity enhanced BCHA production by reducing BCAA biosynthesis, which occurs via a pathway that directly competes with BCHA production.

IMPORTANCE Recently, several studies have attempted to increase the production of branched-chain higher alcohols (BCHAs) in the yeast Saccharomyces cerevisiae. The key enzymes for BCHA biosynthesis in S. cerevisiae are the branched-chain amino acid aminotransaminases (BCATs) Bat1 and Bat2. Deletion or overexpression of the genes encoding BCATs has an impact on the production of BCHAs; however, amino acid substitution variants of Bat1 and Bat2 that could affect enzymatic properties—and ultimately BCHA productivity—have not been fully studied. By using in silico analysis, we designed variants of Bat1 and Bat2 and expressed them in yeast cells. We found that the engineered BCATs decreased catalytic activities and increased BCHA production. Our approach provides new insight into the functions of BCATs and will be useful in the future construction of enzymes optimized for high-level production of BCHAs.

Simultaneously deleting ADH2 and THI3 genes of Saccharomyces cerevisiae for reducing the yield of acetaldehyde and fusel alcohols

The reduced yields of acetaldehyde and fusel alcohols through fermentation by Saccharomyces cerevisiae is of significance for the improvement of the flavor and health of alcoholic beverages. In this study, the ADH2 (encode alcohol dehydrogenase) and THI3 (encode decarboxylase) genes of the industrial diploid strain S. cerevisiae XF1 were deleted. Results showed that single-gene-deletion mutants by separate gene deletion of ADH2 or THI3 led to a reduced production of the acetaldehyde or fusel alcohols, respectively. In the meantime, the double-gene-deletion mutant S. cerevisiae XF1-AT was constructed by deleting the ADH2 and THI3 simultaneously. An equivalent level of the ethanol production by the S. cerevisiae XF1-AT could be achieved but with the yields of acetaldehyde, isoamyl alcohol and iso-butanol reduced by 42.09%, 15.65% and 20.16%, respectively. In addition, there was no interaction between the ADH2 deletion and THI3 deletion in reducing the production of acetaldehyde and fusel alcohols. The engineered S. cerevisiae XF1-AT provided a new strategy to alcoholic beverages brewing industry for reducing the production of acetaldehyde as well as the fusel alcohols.

Truth in wine yeast

Evolutionary history and early association with anthropogenic environments have made Saccharomyces cerevisiae the quintessential wine yeast. This species typically dominates any spontaneous wine fermentation and, until recently, virtually all commercially available wine starters belonged to this species. The Crabtree effect, and the ability to grow under fully anaerobic conditions, contribute decisively to their dominance in this environment. But not all strains of Saccharomyces cerevisiae are equally suitable as starter cultures. In this article, we review the physiological and genetic characteristics of S. cerevisiae wine strains, as well as the biotic and abiotic factors that have shaped them through evolution. Limited genetic diversity of this group of yeasts could be a constraint to solving the new challenges of oenology. However, research in this field has for many years been providing tools to increase this diversity, from genetic engineering and classical genetic tools to the inclusion of other yeast species in the catalogues of wine yeasts. On occasion, these less conventional species may contribute to the generation of interspecific hybrids with S. cerevisiae. Thus, our knowledge about wine strains of S. cerevisiae and other wine yeasts is constantly expanding. Over the last decades, wine yeast research has been a pillar for the modernisation of oenology, and we can be confident that yeast biotechnology will keep contributing to solving any challenges, such as climate change, that we may face in the future.

Effect of the Deletion of Genes Related to Amino Acid Metabolism on the Production of Higher Alcohols by Saccharomyces cerevisiae

The higher alcohols produced by Saccharomyces cerevisiae exert remarkable influence on the taste and flavour of Chinese Baijiu. In order to study the regulation mechanism of amino acid metabolism genes on higher alcohol production, eight recombinant strains with amino acid metabolism gene deletion were constructed. The growth, fermentation performance, higher alcohol production, and expression level of genes in recombinant and original α5 strains were determined. Results displayed that the total higher alcohol concentration in α5ΔGDH1 strain decreased by 27.31% to 348.68 mg/L compared with that of α5. The total content of higher alcohols in α5ΔCAN1 and α5ΔGAT1 strains increased by 211.44% and 28.36% to 1493.96 and 615.73 mg/L, respectively, compared with that of α5. This study is the first to report that the CAN1 and GAT1 genes have great influence on the generation of higher alcohols. The results demonstrated that amino acid metabolism plays a substantial role in the metabolism of higher alcohols by S. cerevisiae. Interestingly, we also found that gene knockout downregulated the expression levels of the knocked out gene and other genes in the recombinant strain and thus affected the formation of higher alcohols by S. cerevisiae. This study provides worthy insights for comprehending the metabolic mechanism of higher alcohols in S. cerevisiae for Baijiu fermentation.

An efficient method to produce 1,4-pentanediol from the biomass of the algae Chlorella ohadi with levulinic acid as intermediate

Today, the development of innovative methods for production of organic compounds from natural resources is essential topic for many research groups in the worldwide. Levulinic acid is a platform for many important organic processes in the synthesis of natural products, pharmaceuticals, plasticizers, drugs and various other additives. In addition, 1,4-pentanediol which is a product of reduction of levulinic acid, is a valuable raw material in the chemical industry. Here, we report a highly efficient method for the production of levulinic acid from Chlorella ohadi algae using hydrothermal hydrolysis process by using HCl. Our methodology shows that the levulinic acid can be obtained in almost 90% molar yield compared to the glucose in Chlorella ohadi. Finally, we describe a one step reaction for the completely conversion of levulinic acid into 1,4-pentadiol in water using S. cerevisiae yeast as a catalyst.

Saccharomyces cerevisiae and its industrial applications

Saccharomyces cerevisiae is the best studied eukaryote and a valuable tool for most aspects of basic research on eukaryotic organisms. This is due to its unicellular nature, which often simplifies matters, offering the combination of the facts that nearly all biological functions found in eukaryotes are also present and well conserved in S. cerevisiae. In addition, it is also easily amenable to genetic manipulation. Moreover, unlike other model organisms, S. cerevisiae is concomitantly of great importance for various biotechnological applications, some of which date back to several thousands of years. S. cerevisiae's biotechnological usefulness resides in its unique biological characteristics, i.e., its fermentation capacity, accompanied by the production of alcohol and CO2 and its resilience to adverse conditions of osmolarity and low pH. Among the most prominent applications involving the use of S. cerevisiae are the ones in food, beverage -especially wine- and biofuel production industries. This review focuses exactly on the function of S. cerevisiae in these applications, alone or in conjunction with other useful microorganisms involved in these processes. Furthermore, various aspects of the potential of the reservoir of wild, environmental, S. cerevisiae isolates are examined under the perspective of their use for such applications.

[Synthesis and regulation of flavor compounds derived from brewing yeast: fusel alcohols]

Among the main beer components, fusel alcohols are important because of their influence on the flavor of the final product, and therefore on its quality. During the production process, these compounds are generated by yeasts through the metabolism of amino acids. The yeasts, fermentation conditions and wort composition affect fusel alcohols profiles and their concentrations. In this review, we provide detailed information about the enzymes involved in fusel alcohols formation and their regulation. Moreover, we describe how the type of yeast used, the fermentation temperature and the composition of carbohydrates and nitrogen source in wort, among other fermentation parameters, affect the biosynthesis of these alcohols. Knowing how fusel alcohol levels vary during beer production provides a relevant tool for brewers to achieve the desired characteristics in the final product and at the same time highlights the aspects still unknown to science.

The molecular biology of fruity and floral aromas in beer and other alcoholic beverages

Aroma compounds provide attractiveness and variety to alcoholic beverages. We discuss the molecular biology of a major subset of beer aroma volatiles, fruity and floral compounds, originating from raw materials (malt and hops), or formed by yeast during fermentation. We introduce aroma perception, describe the most aroma-active, fruity and floral compounds in fruits and their presence and origin in beer. They are classified into categories based on their functional groups and biosynthesis pathways: (1) higher alcohols and esters, (2) polyfunctional thiols, (3) lactones and furanones, and (4) terpenoids. Yeast and hops are the main sources of fruity and flowery aroma compounds in beer. For yeast, the focus is on higher alcohols and esters, and particularly the complex regulation of the alcohol acetyl transferase ATF1 gene. We discuss the release of polyfunctional thiols and monoterpenoids from cysteine- and glutathione-S-conjugated compounds and glucosides, respectively, the primary biological functions of the yeast enzymes involved, their mode of action and mechanisms of regulation that control aroma compound production. Furthermore, we discuss biochemistry and genetics of terpenoid production and formation of non-volatile precursors in Humulus lupulus (hops). Insight in these pathways provides a toolbox for creating innovative products with a diversity of pleasant aromas.

Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae

Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14, encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5′ sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr⁷³ residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates that AAD genes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeast AAD genes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeast AAD gene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role for AAD genes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications.

IMPORTANCE Functional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the first Saccharomyces cerevisiae genome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-member AAD family. Here, we demonstrate that proteins encoded by two members of this family exhibit aliphatic and aryl-aldehyde reductase activity, and further that such activity can be recovered from pseudogenized AAD genes via ancestral-state reconstruction. The phylogeny of yeast AAD genes suggests that these proteins may have played an important ancestral role in detoxifying aromatic aldehydes in ligninolytic fungi. However, in yeast adapted to niches rich in sugars, AAD genes become subject to mutational erosion. Our findings shed new light on the selective pressures and molecular mechanisms by which genes undergo pseudogenization.

Screening of Debaryomyces hansenii Strains for Flavor Production under a Reduced Concentration of Nitrifying Preservatives Used in Meat Products

A total of 15 Debaryomyces hansenii strains from different food origins were genetically characterized and tested on a culture medium resembling the composition of fermented sausages but different concentrations of nitrifying preservatives. Genetic typing of the D. hansenii strains revealed two levels of discrimination: isolation source or strain specific. Different abilities to proliferate on culture media containing different concentrations of nitrate and nitrite, as sole nitrogen sources and in the presence of amino acids, were observed within D. hansenii strains. Overall metabolism of amino acids and generation of aroma compounds were related to the strain origin of isolation. The best producers of branched aldehydes and ethyl ester compounds were strains isolated from pork sausages. Strains from cheese and llama sausages were good producers of ester compounds and branched alcohols, while vegetable strains produced mainly acid compounds. Nitrate and nitrite reduction affected in different ways the production of volatiles by D. hansenii.

Branched-Chain Aminotransferases Control TORC1 Signaling in Saccharomyces cerevisiae

The conserved target of rapamycin complex 1 (TORC1) integrates nutrient signals to orchestrate cell growth and proliferation. Leucine availability is conveyed to control TORC1 activity via the leu-tRNA synthetase/EGOC-GTPase module in yeast and mammals, but the mechanisms sensing leucine remain only partially understood. We show here that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, effectively activate the yeast TORC1 kinase via both EGOC GTPase-dependent and -independent mechanisms. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT), which in yeast are represented by the mitochondrial and cytosolic enzymes Bat1 and Bat2, respectively. BCAT yeast mutants exhibit severely compromised TORC1 activity, which is partially restored by expression of Bat1 active site mutants, implicating both catalytic and structural roles of BCATs in TORC1 control. We find that Bat1 interacts with branched-chain amino acid metabolic enzymes and, in a leucine-dependent fashion, with the tricarboxylic acid (TCA)-cycle enzyme aconitase. BCAT mutation perturbed TCA-cycle intermediate levels, consistent with a TCA-cycle block, and resulted in low ATP levels, activation of AMPK, and TORC1 inhibition. We propose the biosynthetic capacity of BCAT and its role in forming multicomplex metabolons connecting branched-chain amino acids and TCA-cycle metabolism governs TCA-cycle flux to activate TORC1 signaling. Because mammalian mitochondrial BCAT is known to form a supramolecular branched-chain α-keto acid dehydrogenase enzyme complex that links leucine metabolism to the TCA-cycle, these findings establish a precedent for understanding TORC1 signaling in mammals.

In all organisms from yeasts to mammals the target of rapamycin TORC1 pathway controls growth in response to nutrients such as leucine, but the leucine sensing mechanisms are only partially characterized. We show that both leucine and its α-ketoacid metabolite, α-ketoisocaproate, are similarly capable of activating TORC1 kinase via EGOC GTPase-dependent and -independent mechanisms. Activation of TORC1 by leucine or α-ketoisocaproate is only partially mediated via EGOC-GTPase. Leucine and α-ketoisocaproate are interconverted by ubiquitous branched-chain aminotransferases (BCAT). Disruption of BCAT caused reduced TORC1 activity, which was partially restored by expression of BCAT active site mutants, arguing for both structural and catalytic roles of BCAT in TORC1 control. We find BCAT interacts with several branched-chain amino acid metabolic enzymes, and in a leucine-dependent fashion with the tricarboxylic acid (TCA)-cycle enzyme aconitase. Both aconitase mutation or TCA-cycle inhibition impaired TORC1 activity. Mutation of BCAT resulted in a TCA-cycle intermediate profile consistent with a TCA-cycle block, low ATP levels, activation of AMPK, and TORC1 inhibition. Our results suggest a model whereby BCAT coordinates leucine and TCA cycle metabolism to control TORC1 signaling. Taken together, our findings forge key insights into how the TORC1 signaling cascade senses nutrients to control cell growth.

Brettanomyces yeasts--From spoilage organisms to valuable contributors to industrial fermentations

Ever since the introduction of controlled fermentation processes, alcoholic fermentations and Saccharomyces cerevisiae starter cultures proved to be a match made in heaven. The ability of S. cerevisiae to produce and withstand high ethanol concentrations, its pleasant flavour profile and the absence of health-threatening toxin production are only a few of the features that make it the ideal alcoholic fermentation organism. However, in certain conditions or for certain specific fermentation processes, the physiological boundaries of this species limit its applicability. Therefore, there is currently a strong interest in non-Saccharomyces (or non-conventional) yeasts with peculiar features able to replace or accompany S. cerevisiae in specific industrial fermentations. Brettanomyces (teleomorph: Dekkera), with Brettanomyces bruxellensis as the most commonly encountered representative, is such a yeast. Whilst currently mainly considered a spoilage organism responsible for off-flavour production in wine, cider or dairy products, an increasing number of authors report that in some cases, these yeasts can add beneficial (or at least interesting) aromas that increase the flavour complexity of fermented beverages, such as specialty beers. Moreover, its intriguing physiology, with its exceptional stress tolerance and peculiar carbon- and nitrogen metabolism, holds great potential for the production of bioethanol in continuous fermentors. This review summarizes the most notable metabolic features of Brettanomyces, briefly highlights recent insights in its genetic and genomic characteristics and discusses its applications in industrial fermentation processes, such as the production of beer, wine and bioethanol.

Saccharomyces cerevisiae mitochondria are required for optimal attractiveness to Drosophila melanogaster

While screening a large collection of wild and laboratory yeast strains for their ability to attract Drosophila melanogaster adults, we noticed a large difference in fly preference for two nearly isogenic strains of Saccharomyces cerevisiae, BY4741 and BY4742. Using standard genetic analyses, we tracked the preference difference to the lack of mitochondria in the BY4742 strain used in the initial experiment. We used gas chromatography coupled with mass spectroscopy to examine the volatile compounds produced by BY4741 and the mitochondria-deficient BY4742, and found that they differed significantly. We observed that several ethyl esters are present at much higher levels in strains with mitochondria, even in fermentative conditions. We found that nitrogen levels in the substrate affect the production of these compounds, and that they are produced at the highest level by strains with mitochondria when fermenting natural fruit substrates. Collectively these observations demonstrate that core metabolic processes mediate the interaction between yeasts and insect vectors, and highlight the importance mitochondrial functions in yeast ecology.

An indirect assay for volatile compound production in yeast strains

Traditional flavor analysis relies on gas chromatography coupled to mass spectrometry (GC-MS) methods. Here we describe an indirect method coupling volatile compound formation to an ARO9-promoter-LacZ reporter gene. The resulting β-galactosidase activity correlated well with headspace solid phase micro extraction (HS/SPME) GC-MS data, particularly with respect to the formation of rose flavor. This tool enables large-scale screening of yeast strains and their progeny to identify the most flavor active strains.