Research Articles (Institute for Wine Biotechnology)
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- Item3-way networks : application of hypergraphs for modelling increased complexity in comparative genomics(PLoS, 2015-03) Weighill, Deborah A.; Jacobson, Daniel A.We present and develop the theory of 3-way networks, a type of hypergraph in which each edge models relationships between triplets of objects as opposed to pairs of objects as done by standard network models. We explore approaches of how to prune these 3-way networks, illustrate their utility in comparative genomics and demonstrate how they find relationships which would be missed by standard 2-way network models using a phylogenomic dataset of 211 bacterial genomes.
- ItemBiogenic amines in wine : understanding the headache(SASEV, 2008-09) Smit, A. Y.; Du Toit, W. J.; Du Toit, M.The presence of biogenic amines in wine is becoming increasingly important to consumers and producers alike, due to the potential threats of toxicity to humans and consequent trade implications. In the scientific field, biogenic amines have the potential to be applied as indicators of food spoilage and/or authenticity. Biogenic amines can be formed from their respective amino acid precursors by various microorganisms present in the wine, at any stage of production, ageing or storage. To understand the large number of factors that could influence the formation of biogenic amines, the chemical, biochemical, enzymatic and genetic properties relating to these compounds have to be considered. Analytical and molecular methods to detect biogenic amines in wine, as well as possibilities that could enable better control over their production levels in wine will also be explored in this review.
- ItemCarnitine requires choline to exert physiological effects in saccharomyces cerevisiae(Frontiers Media, 2018-07-02) Du Plessis, Michelle; Franken, Jaco; Bauer, Florian; De Biase, DanielaL-Carnitine is a key metabolite in the energy metabolism of eukaryotic cells, functioning as a shuttling molecule for activated acyl-residues between cellular compartments. In higher eukaryotes this function is essential, and defects in carnitine metabolism has severe effects on fatty acid and carbon metabolism. Carnitine supplementation has been associated with an array of mostly beneficial impacts in higher eukaryotic cells, including stress protection and regulation of redox metabolism in diseased cells. Some of these phenotypes have no obvious link to the carnitine shuttle, and suggest that carnitine has as yet unknown shuttle-independent functions. The existence of shuttle-independent functions has also been suggested in Saccharomyces cerevisiae, including a beneficial effect during hydrogen peroxide stress and a detrimental impact when carnitine is co-supplemented with the reducing agent dithiothreitol (DTT). Here we used these two distinct yeast phenotypes to screen for potential genetic factors that suppress the shuttle independent physiological effects of carnitine. Two deletion strains, Δcho2 and Δopi3, coding for enzymes that catalyze the sequential conversion of phosphatidylethanolamine to phosphatidylcholine were identified for suppressing the phenotypic effects of carnitine. Additional characterisation indicated that the suppression cannot be explained by differences in phospholipid homeostasis. The phenotypes could be reinstated by addition of extracellular choline, but show that the requirement for choline is not based on some overlapping function or the structural similarities of the two molecules. This is the first study to suggest a molecular link between a specific metabolite and carnitine-dependent, but shuttle-independent phenotypes in eukaryotes.
- ItemCharacterisation of non-saccharomyces yeasts using different methodologies and evaluation of their compatibility with malolactic fermentation(South African Society for Enology and Viticulture, 2017) Du Plessis, H. W.; Du Toit, M.; Hoff, J. W.; Hart, R. S.; Ndimba, B. K.; Jolly, N. P.Although Saccharomyces cerevisiae is the yeast species predominantly used for alcoholic fermentation, non-Saccharomyces yeast species are also important because they produce secondary metabolites that can contribute to the final flavour and taste of wines. In this study, 37 strains representing seven non-Saccharomyces species were characterised and evaluated for potential use in wine production, as well as for their effects on malolactic fermentation (MLF). Contour-clamped homogeneous electric field (CHEF) gel electrophoresis and matrix-assisted laser desorption ionisation using a time-of-flight mass spectrometer (MALDI-TOF MS) were used to verify species identity and to determine intra-species variation. Extracellular enzyme production, malic acid degradation and the fermentation kinetics of the yeasts were also investigated. CHEF karyotyping and MALDI-TOF MS were useful for identifying and typing Hanseniaspora uvarum, Lachancea thermotolerans, Candida zemplinina (synonym: Starmerella bacillaris) and Torulaspora delbrueckii strains. Only H. uvarum and Metschnikowia pulcherrima strains were found to have β-glucosidase activity. M. pulcherrima strains also had protease activity. Most of the strains showed limited malic acid degradation, and only Schizosaccharomyces pombe and the C. zemplinina strains showed mentionable degradation. In synthetic wine fermentations, C. stellata, C. zemplinina, H. uvarum, M. pulcherrima and Sc. pombe strains were shown to be slow to medium fermenters, whereas L. thermotolerans and T. delbrueckii strains were found to be medium to strong fermenters. The effect of the yeasts on MLF varied, but inhibition was strain dependent.
- ItemDetermining the impact of industrial wine yeast strains on organic acid production under white and red wine-like fermentation conditions(South African Society for Enology and Viticulture, 2015) Chidi, B. S.; Rossouw, D.; Buica, A. S.; Bauer, FlorianOrganic acids are a major contributor to wine flavour and aroma. In the past, the scientific focus has mostly been on organic acids derived from grapes or on the transformation of malic acid to lactic acid by lactic acid bacteria, since these acids contribute significantly to the final total acidity of wine. However, the organic acid concentration and composition also change significantly during alcoholic fermentation, yet only limited information regarding the impact of different yeast strains on these changes has been published. Here we report on changes in organic acid (malic, tartaric, citric, succinic, acetic and pyruvic) composition during fermentation by five widely used industrial wine yeast strains in a synthetic grape must (MS300) reflecting two very different, but both wine-like, fermentation conditions. Samples were obtained from three physiological stages during fermentation, namely the exponential growth phase (day 2), early stationary phase (day 5) and late stationary phase (day 14). These different stages were selected to provide more information on acid evolution throughout fermentation, as well as on the impact of nutritional and environmental conditions during aerobic and anaerobic fermentation. Among other observations, some strains (such as VIN13 and 285) were shown to be generally higher producers of most acids in white and/ or red wine fermentation settings, while other strains (such as DV10) were generally lower acid producers. The data clearly demonstrate that different strains have different acid consumption and production patterns, and this presents a first step towards enabling winemakers to appropriately select strains for acid management during fermentation.
- ItemThe diversity and dynamics of indigenous yeast communities in grape must from vineyards employing different agronomic practices and their influence on wine fermentation(South African Society for Enology and Viticulture, 2015) Bagheri, Bahareh; Bauer, Florian; Setati, M. E.The current study evaluated the diversity of yeast species in Cabernet Sauvignon grape must derived from three neighbouring vineyards from a similar terroir but on which significantly different management practices are employed. The fermentation kinetics and yeast population dynamics were monitored from the beginning to the end of spontaneous fermentation. The grape musts were characterised by distinct yeast populations comprising oxidative, weakly fermentative and strongly fermentative yeasts. Different combinations of dominant non-Saccharomyces yeasts were observed in each must, with significantly different assortments of dominant species, including Starmerella bacillaris (synonym Candida zemplinina), Lachancea thermotolerans, Hanseniaspora uvarum, Candida parapsilosis and Wickerhamomyces anomalus. None of these yeast consortia appeared to affect the growth of Saccharomyces cerevisiae or inhibit the overall progress of fermentation. However, the percentage of fermentative yeasts was positively correlated with the fermentation rate. Glucose and fructose consumption rates suggested active participation of both glucophilic and fructophilic yeasts from the onset of fermentation. The data highlight two parameters, viz. initial cell concentration and yeast community composition, as important fermentation drivers and open the possibility to predict fermentation behaviour based on the initial composition of the yeast community.
- ItemEffect of different extraction methods on the quality and biochemical attributes of pomegranate juice and the application of Fourier transformed infrared spectroscopy in discriminating between different extraction methods(Frontiers Media, 2021-08-23) Arendse, Ebrahiema; Nieuwoudt, Helene; Fawole, Olaniyi Amos; Linus Opara, UmezuruikeThis study investigated the effects of extraction methods on the physicochemical, phytochemical, and antioxidant properties of pomegranate juice (cv. Wonderful). In addition, the application of attenuated total reflectance Fourier transformed mid-infrared (ATR-FT-MIR) spectroscopy and chemometrics were explored in order to discriminate between different extraction methods. Juice variants evaluated included juice extracted without crushing the seeds (arils only) using a juice extractor (JE), juice extracted by crushing the seeds using a blender (arils plus seed) (JB), and juice extracted from half fruit using a commercial hand press juicer (CH). Juice extracted from CH had higher total soluble solid (TSS) content (18.20%), TSS/TA ratio (15.83), and color properties (a* = 32.67, b* = 11.80, C* = 34.77) compared with extraction methods JE and JB. The juice extracted from JB showed the highest titratable acidity (2.17%), cloudiness (0.43), and lowest pH value (2.69). The total phenolics and anthocyanin content in the investigated juice ranged from 1.87 to 3.04 g gallic acid equivalent (GAE)/L and 37.74–43.67 mg cyanidin 3-glucoside equivalent/L of crude juice, respectively. Juice extracted from JB and CH was significantly higher in phenolic and anthocyanin compared with JE. Orthogonal partial least squares discriminant analysis (OPLS-DA) and principal component analysis (PCA) were used for classification. Classification accuracy of 100% was achieved between the three methods. The S-line plot revealed that the corresponding wavelength bands within the following regions 1,090, 1,250, 1,750, and 3,200 cm−1 were responsible for discrimination between the different extraction methods. Our results suggest that the main contributor to the discrimination between extraction methods were TSS, TSS/TA, color attributes, and anthocyanin content. Overall, this study has demonstrated that ATR-FT-MIR spectroscopy provides a powerful way to discriminate between juice extraction methods.
- ItemEnzymes in winemaking : harnessing natural catalysts for efficient biotransformations(South African Society for Enology and Viticulture, 2000) Van Rensburg, P.; Pretorius, I. S.Enzymes play a definitive role in the ancient and complex process of winemaking. From a scientific and technical point of view, wine can be seen as the product of enzymatic transformation of grape juice. From the pre-fermentation stage, through fermentation, post-fermentation and aging, enzymes are the major driving forces catalysing various biotransformation reactions. These biocatalysts originate not only from the grape itself but also from yeasts and other microbes (fungi and bacteria) associated with vineyards and wine cellars. Through better understanding of these enzymatic activities, winemakers have come to learn how to control the unwanted enzymes while optimising the desired activities. Today, winemakers reinforce and extend the action of these endogenous enzymes by the judicious application of an ever-increasing spectrum of commercial enzyme preparations. These enzyme preparations are applied to winemaking with the aims of improving the clarification and processing of wine, releasing varietal aromas from precursor compounds, reducing ethyl carbamate formation and lowering alcohol levels. This review article summarises the most important enzymes applied to winemaking, the nature and structure of their substrates, and the reactions catalysed by these enzymes. This paper also reviews the limitations of the endogenous enzymes derived from grapes and microbes present in must and wine, along with the effects of commercial enzyme preparations on process technology and the quality of the final product. Prospects of developing wine yeast strains expressing tailored enzymes are also highlighted.
- ItemGenetic improvement of grapevine : tailoring grape varieties for the third millennium(South African Society of Enology and Viticulture, 2000) Vivier, M. A.; Pretorius, I. S.The remarkable propagative aptitute of grapevine is one of the key factors contributing to its success as a cultivated species and to the spread of the domesticated grapevine, establishing it as one of the most important fruit species worldwide. Today there are some 8 million hectares of vineyards across the world. It is therefore titting that the successful implementation of the powerful technology of gene manipulation in grapevine is to a large extent reliant on this regenerative ability. Currently, several varieties of grapevines have been successfully genetically transformed, largely by employing somatic embryogenesis to generate highly regenerative target material. Especially attractive in the wine industry is the possibility of improving grapevine varieties by the addition of genes that confer useful traits, such as resistances against biotic and abiotic factors and manipulation of certain metabolic functions. In principle, gene transfer technology allows for the directed manipulation of a specific trait without altering the characteristic nature of the cultivar, permitting the improvement of the traditional cultivars while maintaining their established varietal characteristics. For the most part, targeted traits currently include disease resistance and improved berry quality. The promise of this technology is threatened by worldwide resistance to genetically modified organisms, and in the wine industry by complications surrounding the property rights and naming of transgenic vines. If it is not possible to maintain the varietal name when a transgenic vine has the same properties as the original well known variety, the significant advantages of gene technology over traditional breeding programmes are to a large extent lost. If these and other complications can be overcome, the integration of this powerful technology with traditional breeding programmes, and with other initiatives such as the study of the grapevine genome, will ensure a new era in the cultivation of this ancient species.
- ItemDie genetiese verbetering van wyndruifkultivars en wyngisrasse vir 'n markgerigte wynbedryf : nuwe benaderings tot die oeroue kuns van wynbereiding(AOSIS OpenJournals, 2003) Pretorius, I. S.The widening gap between wine production and wine consumption, the shift of consumer preferences away from basic commodity wine to top quality wine, and the gruelling competition brought about by economic globalisation call for a total revolution in the magical world of wine. In the process of transforming the wine industry from a production-driven industry to a market-orientated enterprise, there is an increasing dependence on, amongst others, biotechnological innovation to launch the wine industry with a quantum leap across the formidable market challenges of the 21st century. Market-orientated designer grape cultivars and wine yeast strains are currently being genetically programmed with surgical precision for the cost-competitive production of high quality grapes and wine with relatively minimal resource inputs and a low environmental impact. With regard to Grapevine Biotechnology, this entails the establishment of stress tolerant and disease resistant varieties of Vitis vinifera with increased productivity, efficiency, sustainability and environmental friendliness, especially regarding improved pest and disease control, water use efficiency and grape quality. With regard to Wine Yeast Biotechnology, the emphasis is on the development of Saccharomyces cerevisiae strains with improved fermentation, processing and biopreservation abilities, and capacities for an increase in the wholesomeness and sensory quality of wine. The successful commercialisation of transgenic grape cultivars and wine yeasts depends on a number of scientific, technical, safety, ethical, legal, economic and marketing factors, and it therefore will be unwise to entertain high expectations in the short term. However, in the light of the phenomenal potential advantages of tailor-made grape varieties and yeast strains, it would be equally self-destructive in the long term if this strategically important “life insurance policy” is not taken out by the wine industry. This overview highlights the most important examples of the way in which V. vinifera grape varieties and S. cerevisiae wine yeast strains are currently being designed with surgical precision on the basis of market demand for the cost-effective, sustainable and environmentally friendly production of healthy, top quality grapes and wine.
- ItemThe grapevine and wine microbiome : insights from high-throughput amplicon sequencing(Frontiers Media, 2017) Morgan, Horatio H.; Du Toit, Maret; Setati, Mathabatha E.From the time when microbial activity in wine fermentation was first demonstrated, the microbial ecology of the vineyard, grape, and wine has been extensively investigated using culture-based methods. However, the last 2 decades have been characterized by an important change in the approaches used for microbial examination, due to the introduction of DNA-based community fingerprinting methods such as DGGE, SSCP, T-RFLP, and ARISA. These approaches allowed for the exploration of microbial community structures without the need to cultivate, and have been extensively applied to decipher the microbial populations associated with the grapevine as well as the microbial dynamics throughout grape berry ripening and wine fermentation. These techniques are well-established for the rapid more sensitive profiling of microbial communities; however, they often do not provide direct taxonomic information and possess limited ability to detect the presence of rare taxa and taxa with low abundance. Consequently, the past 5 years have seen an upsurge in the application of high-throughput sequencing methods for the in-depth assessment of the grapevine and wine microbiome. Although a relatively new approach in wine sciences, these methods reveal a considerably greater diversity than previously reported, and identified several species that had not yet been reported. The aim of the current review is to highlight the contribution of high-throughput next generation sequencing and metagenomics approaches to vineyard microbial ecology especially unraveling the influence of vineyard management practices on microbial diversity.
- ItemIdentifying genes that impact on aroma profiles produced by Saccharomyces cerevisiae and the production of higher alcohols(Springer-Verslag, 2011-05) Styger, Gustav; Jacobson, Dan; Bauer, FlorianDuring alcoholic fermentation, many volatile aroma compounds are formed by Saccharomyces cerevisiae, including esters, fatty acids, and higher alcohols. While the metabolic network that leads to the formation of these compounds is reasonably well mapped, surprisingly little is known about specific enzymes involved in specific reactions, the regulation of the network, and the physiological roles of individual pathways within the network. Furthermore, different yeast strains tend to produce significantly different aroma profiles. These differences are of tremendous biotechnological interest, since producers of alcoholic beverages such as wine and beer are searching for means to diversify and improve their product range. Various factors such as the redox, energy, and nutritional balance of a cell have previously been suggested to directly or indirectly affect and regulate the network. To gain a better understanding of the regulations and physiological role of this network, we screened a subset of the EUROSCARF strain deletion library for genes that, when deleted, would impact most significantly on the aroma profile produced under fermentative conditions. The 10 genes whose deletion impacted most significantly on higher alcohol production were selected and further characterized to assess their mode of action within or on this metabolic network. This is the first description of a large-scale screening approach using aroma production as the primary selection criteria, and the data suggest that many of the identified genes indeed play central and direct roles within the aroma production network of S. cerevisiae.
- ItemImpact of grape temperature at pressing on organic acids and oenological characteristics of Méthode Cap Classique wines(South African Society for Enology and Viticulture, 2018) Chidi, B. S.; Mafata, M.; Notshokovu, N. Z.; Van Jaarsveld, F.Maintaining the chemical composition of a wine is essential for the wine industry. Although the sugar-acid balance of a wine is of primary sensory importance, individual acids and oenological parameters are equally important. The main focus of this study was to investigate the impact of grape temperature at harvest, on the oenological volatile acidity (VA), titratable acidity (TA), pH and alcohol levels and organic acid (citric, malic, pyruvic and succinic) characteristics of Méthode Cap Classique (MCC) wines during winemaking, produced from grape cultivars obtained from two regions. Chardonnay and Pinot noir grapes were obtained from Robertson (warmer) and Elgin (cooler) regions and were subjected to different temperature treatments, i.e. 0, 10, 25 and 30oC before further processing, including pressing, primary fermentation, blending, tirage, secondary fermentation, riddling and disgorging. Grape temperature was mostly responsible for a significantly higher pH of Robertson (0 and 10ºC) and lower pH (0ºC) of Elgin post-tirage wines. Chardonnay base wines from both regions that were vinified from grapes at lower temperatures (0 and 10oC) were richer in malic- and succinic acid, while Pinot noir wines from both regions were characterised by higher malic-, citric- and pyruvic acid. Pyruvic acid was only detected after the secondary fermentations in wines from both regions. To our knowledge, this study is the first to investigate the influence of grape temperature on the oenological and organic acid characteristics of MCC wines in different regions, and throughout different production stages.
- ItemThe impact of single amino acids on growth and volatile aroma production by Saccharomyces cerevisiae strains(Frontiers Media, 2017) Fairbairn, Samantha; McKinnon, Alexander; Musarurwa, Hannibal T.; Ferreira, Antonio C.; Bauer, Florian; Lanciotti, RosalbaNitrogen availability and utilization by Saccharomyces cerevisiae significantly influence fermentation kinetics and the production of volatile compounds important for wine aroma. Amino acids are the most important nitrogen source and have been classified based on how well they support growth. This study evaluated the effect of single amino acids on growth kinetics and major volatile production of two phenotypically different commercial wine yeast strains in synthetic grape must. Four growth parameters, lag phase, maximum growth rate, total biomass formation and time to complete fermentation were evaluated. In contrast with previous findings, in fermentative conditions, phenylalanine and valine supported growth well and asparagine supported it poorly. The four parameters showed good correlations for most amino acid treatments, with some notable exceptions. Single amino acid treatments resulted in the predictable production of aromatic compounds, with a linear correlation between amino acid concentration and the concentration of aromatic compounds that are directly derived from these amino acids. With the increased complexity of nitrogen sources, linear correlations were lost and aroma production became unpredictable. However, even in complex medium minor changes in amino acid concentration continued to directly impact the formation of aromatic compounds, suggesting that the relative concentration of individual amino acids remains a predictor of aromatic outputs, independently of the complexity of metabolic interactions between carbon and nitrogen metabolism and between amino acid degradation and utilization pathways.
- ItemInvestigating the concept of South African old vine Chenin blanc(South African Society for Enology and Viticulture, 2020) Mafata, M.; Brand, J.; Panzeri, V.; Buica, A. S.Although South African vineyards are still young by European standards, there is a belief in the industry that vines aged 35 or more years produce grapes and wines with specific characteristics (“old vine wines”). The aim of this study was to investigate the existence of the concept of old vine Chenin blanc wines using a typicality rating and sorting tasks. Chenin blanc wines were made from grapes harvested from vines aged five to 45 years old. Winemaking was standardised, with no wood contact. Typicality rating and sorting tasks were performed on young (first-stage) and two-year bottle-aged (second-stage) wines. Principal component analysis (PCA) on rating data demonstrated judge consensus, but no correlation was found between vine age and typicality rating. Sorting results were submitted to agglomerative hierarchical clustering (AHC) performed on the correspondence analysis (CA) and multidimensional scaling (MDS) results for grouping and attributes resulting from the sorting task. The clusters were different for the young wines and two-year bottle-aged wines. The verbal aspect of the sorting demonstrated the judges’ agreement on the concept of old vine Chenin blanc, shown by the annotation of the old vine group as ‘complex’, ‘balance’, ‘rich’ and ‘good mouthfeel’. However, because the judges did not sort the wines according to vine age, the perceptual aspect of the concept could not be confirmed, its features could not be tested further, and the sensory space could not be built.
- ItemInvestigating the effect of selected non-saccharomyces species on wine ecosystem function and major volatiles(Frontiers Media, 2018-11-13) Bagheri, Bahareh; Zambelli, Paolo; Vigentini, Ileana; Bauer, Florian; Setati, Mathabatha Evodia; Cao, MingfengNatural alcoholic fermentation is initiated by a diverse population of several non-Saccharomyces yeast species. However, most of the species progressively die off, leaving only a few strongly fermentative species, mainly Saccharomyces cerevisiae. The relative performance of each yeast species is dependent on its fermentation capacity, initial cell density, ecological interactions as well as tolerance to environmental factors. However, the fundamental rules underlying the working of the wine ecosystem are not fully understood. Here we use variation in cell density as a tool to evaluate the impact of individual non-Saccharomyces wine yeast species on fermentation kinetics and population dynamics of a multi-species yeast consortium in synthetic grape juice fermentation. Furthermore, the impact of individual species on aromatic properties of wine was investigated, using Gas Chromatography-Flame Ionization Detector. Fermentation kinetics was affected by the inoculation treatment. The results show that some non-Saccharomyces species support or inhibit the growth of other non-Saccharomyces species in the multi-species consortium. Overall, the fermentation inoculated with a high cell density of Starmerella bacillaris displayed the fastest fermentation kinetics while fermentation inoculated with Hanseniaspora vineae showed the slowest kinetics. The production of major volatiles was strongly affected by the treatments, and the aromatic signature could in some cases be linked to specific non-Saccharomyces species. In particular, Wickerhamomyces anomalus at high cell density contributed to elevated levels of 2-Phenylethan-1-ol whereas Starm. bacillaris at high cell density resulted in the high production of 2-methylpropanoic acid and 3-Hydroxybutanone. The data revealed possible direct and indirect influences of individual non-Saccharomyces species within a complex consortium, on wine chemical composition.
- ItemIs there a link between coffee aroma and the level of furanmethanethiol (FMT) in pinotage wines(South African Society for Enology and Viticulture, 2020) Garrido-Banuelos, G.; Buica, A. S.Over the years, Pinotage has found its way into the South African and international market. Producers have used the flavour potential of this “original” South African grape to produce different wine styles, one of them being the so-called “coffee-style Pinotage”. The current study aims to explain the impact of furanmethanethiol (FMT) on the characteristic coffee aroma of these coffee-style wines. Chemical and sensory evaluation, as well as data mining of the technical information available, was performed. Not all wines marketed as “coffee Pinotage” showed a high “coffee” rating. However, the results showed a good correlation between the aroma perception and FMT concentrations (R2 = 0.81). However, RV coefficients were low when comparing the coffee rating with the information provided on both the front and the back label, which shows that, in some cases, the use of the “coffee Pinotage” term was rather part of the marketing strategy.
- ItemLinking gene regulation and the exo-metabolome : a comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast(BioMed Central, 2008-11) Rossouw, Debra; Naes, Tormod; Bauer, Florian F.Background: 'Omics' tools provide novel opportunities for system-wide analysis of complex cellular functions. Secondary metabolism is an example of a complex network of biochemical pathways, which, although well mapped from a biochemical point of view, is not well understood with regards to its physiological roles and genetic and biochemical regulation. Many of the metabolites produced by this network such as higher alcohols and esters are significant aroma impact compounds in fermentation products, and different yeast strains are known to produce highly divergent aroma profiles. Here, we investigated whether we can predict the impact of specific genes of known or unknown function on this metabolic network by combining whole transcriptome and partial exo-metabolome analysis. Results: For this purpose, the gene expression levels of five different industrial wine yeast strains that produce divergent aroma profiles were established at three different time points of alcoholic fermentation in synthetic wine must. A matrix of gene expression data was generated and integrated with the concentrations of volatile aroma compounds measured at the same time points. This relatively unbiased approach to the study of volatile aroma compounds enabled us to identify candidate genes for aroma profile modification. Five of these genes, namely YMR210W, BAT1, AAD10, AAD14 and ACS1 were selected for over expression in commercial wine yeast, VIN13. Analysis of the data show a statistically significant correlation between the changes in the exo-metabome of the over expressing strains and the changes that were predicted based on the unbiased alignment of transcriptomic and exo-metabolomic data. Conclusion: The data suggest that a comparative transcriptomics and metabolomics approach can be used to identify the metabolic impacts of the expression of individual genes in complex systems, and the amenability of transcriptomic data to direct applications of biotechnological relevance.
- ItemLinking terpene synthases to sesquiterpene metabolism in grapevine flowers(Frontiers Media, 2019) Smit, Samuel Jacobus; Vivier, Melane Alethea; Young, Philip RichardGrapevine (Vitis vinifera L.) terpene synthases (VviTPS) are responsible for the biosynthesis of terpenic volatiles. Volatile profiling of nine commercial wine cultivars showed unique cultivar-specific variation in volatile terpenes emitted from grapevine flowers. The flower chemotypes of three divergent cultivars, Muscat of Alexandria, Sauvignon Blanc and Shiraz were subsequently investigated at two flower developmental stages (EL-18 and -26). The cultivars displayed unique flower sesquiterpene compositions that changed during flower organogenesis and the profiles were dominated by either (E)-β-farnesene, (E,E)-α-farnesene or (+)-valencene. In silico remapping of microarray probes to VviTPS gene models allowed for a meta-analysis of VviTPS expression patterns in the grape gene atlas to identify genes that could regulate terpene biosynthesis in flowers. Selected sesquiterpene synthase genes were isolated and functionally characterized in three cultivars. Genotypic differences that could be linked to the function of a targeted gene model resulted in the isolation of a novel and cultivar-specific single product sesquiterpene synthase from Muscat of Alexandria flowers (VvivMATPS10), synthesizing (E)-β-farnesene as its major volatile. Furthermore, we identified structural variations (SNPs, InDels and splice variations) in the characterized VviTPS genes that potentially impact enzyme function and/or volatile sesquiterpene production in a cultivar-specific manner.
- ItemModifying Saccharomyces cerevisiae adhesion properties regulates yeast ecosystem dynamics(American Society for Microbiology, 2018-10-24) Rossouw, D.; Meiring, Skye P.; Bauer, FlorianPhysical contact between yeast species, in addition to better-understood and reported metabolic interactions, has recently been proposed to significantly impact the relative fitness of these species in cocultures. Such data have been generated by using membrane bioreactors, which physically separate two yeast species. However, doubts persist about the degree that the various membrane systems allow for continuous and complete metabolic contact, including the exchange of proteins. Here, we provide independent evidence for the importance of physical contact by using a genetic system to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Such adhesion is controlled by a family of structurally related cell wall proteins encoded by the FLO gene family. As previously shown, the expression of specific members of the FLO gene family in Saccharomyces cerevisiae dramatically changes the coadhesion patterns between this yeast and other yeast species. Here, we use this differential aggregation mediated by FLO genes as a model to assess the impact of physical contact between different yeast species on the relative fitness of these species in simplified ecosystems. The identity of the FLO gene has a marked effect on the persistence of specific non-Saccharomyces yeasts over the course of extended growth periods in batch cultures. Remarkably, FLO1 and FLO5 expression often result in opposite outcomes. The data provide clear evidence for the role of physical contact in multispecies yeast ecosystems and suggest that FLO gene expression may be a major factor in such interactions. IMPORTANCE The impact of direct (physical) versus indirect (metabolic) interactions between different yeast species has attracted significant research interest in recent years. This is due to the growing interest in the use of multispecies consortia in bioprocesses of industrial relevance and the relevance of interspecies interactions in establishing stable synthetic ecosystems. Compartment bioreactors have traditionally been used in this regard but suffer from numerous limitations. Here, we provide independent evidence for the importance of physical contact by using a genetic system, based on the FLO gene family, to modify the degree of physical contact and, therefore, the degree of asexual intraspecies and interspecies adhesion in yeast. Our results show that interspecies contact significantly impacts population dynamics and the survival of individual species. Remarkably, different members of the FLO gene family often lead to very different population outcomes, further suggesting that FLO gene expression may be a major factor in such interactions.