Browsing by Author "Rossouw, D."
Now showing 1 - 16 of 16
Results Per Page
- ItemAdjustment of trehalose metabolism in Wine Saccharomyces cerevisiae strains to modify ethanol yields(AMER SOC MICROBIOLOGY, 1752 N ST NW, WASHINGTON, USA, DC, 20036-2904, 2013) Rossouw, D.; Heyns, E. H.; Setati, M. E.; Bosch, S.; Bauer, Florian
- ItemCo-flocculation of yeast species, a new mechanism to govern population dynamics in microbial ecosystems(Public Library of Science, 2015) Rossouw, D.; Bagheri, Bahareh; Setati, Mathabatha Evodia; Bauer, FlorianFlocculation has primarily been studied as an important technological property of Saccharomyces cerevisiae yeast strains in fermentation processes such as brewing and winemaking. These studies have led to the identification of a group of closely related genes, referred to as the FLO gene family, which controls the flocculation phenotype. All naturally occurring S. cerevisiae strains assessed thus far possess at least four independent copies of structurally similar FLO genes, namely FLO1, FLO5, FLO9 and FLO10. The genes appear to differ primarily by the degree of flocculation induced by their expression. However, the reason for the existence of a large family of very similar genes, all involved in the same phenotype, has remained unclear. In natural ecosystems, and in wine production, S. cerevisiae growth together and competes with a large number of other Saccharomyces and many more non-Saccharomyces yeast species. Our data show that many strains of such wine-related non-Saccharomyces species, some of which have recently attracted significant biotechnological interest as they contribute positively to fermentation and wine character, were able to flocculate efficiently. The data also show that both flocculent and non-flocculent S. cerevisiae strains formed mixed species flocs (a process hereafter referred to as co-flocculation) with some of these non-Saccharomyces yeasts. This ability of yeast strains to impact flocculation behaviour of other species in mixed inocula has not been described previously. Further investigation into the genetic regulation of co-flocculation revealed that different FLO genes impact differently on such adhesion phenotypes, favouring adhesion with some species while excluding other species from such mixed flocs. The data therefore strongly suggest that FLO genes govern the selective association of S. cerevisiae with specific species of non-Saccharomyces yeasts, and may therefore be drivers of ecosystem organisational patterns. Our data provide, for the first time, insights into the role of the FLO gene family beyond intraspecies cellular association, and suggest a wider evolutionary role for the FLO genes. Such a role would explain the evolutionary persistence of a large multigene family of genes with apparently similar function.
- ItemComparative 'omic' profiling of industrial wine yeast strains(Stellenbosch : Stellenbosch University, 2009-12) Rossouw, D.; Bauer, Florian; University of Stellenbosch. Faculty of Agrisciences. Dept. of Viticulture and Oenology. Institute for Wine Biotechnology.The main goal of this project was to elucidate the underlying genetic factors responsible for the different fermentation phenotypes and physiological adaptations of industrial wine yeast strains. To address this problem an ‘omic’ approach was pursued: Five industrial wine yeast strains, namely VIN13, EC1118, BM45, 285 and DV10, were subjected to transcriptional, proteomic and exometabolomic profiling during alcoholic fermentation in simulated wine-making conditions. The aim was to evaluate and integrate the various layers of data in order to obtain a clearer picture of the genetic regulation and metabolism of wine yeast strains under anaerobic fermentative conditions. The five strains were also characterized in terms of their adhesion/flocculation phenotypes, tolerance to various stresses and survival under conditions of nutrient starvation. Transcriptional profiles for the entire yeast genome were obtained for three crucial stages during fermentation, namely the exponential growth phase (day 2), early stationary phase (day 5) and late stationary phase (day 14). Analysis of changes in gene expression profiles during the course of fermentation provided valuable insights into the genetic changes that occur as the yeast adapt to changing conditions during fermentation. Comparison of differentially expressed transcripts between strains also enabled the identification of genetic factors responsible for differences in the metabolism of these strains, and paved the way for genetic engineering of strains with directed modifications in key areas. In particular, the integration of exo-metabolite profiles and gene expression data for the strains enabled the construction of statistical models with a strong predictive capability which was validated experimentally. Proteomic analysis enabled correlations to be made between relative transcript abundance and protein levels for approximately 450 gene and protein pairs per analysis. The alignment of transcriptome and proteome data was very accurate for interstrain comparisons. For intrastrain comparisons, there was almost no correlation between trends in protein and transcript levels, except in certain functional categories such as metabolism. The data also provide interesting insights into molecular evolutionary mechanisms that underlie the phenotypic diversity of wine yeast strains. Overall, the systems biology approach to the study of yeast metabolism during alcoholic fermentation opened up new avenues for hypothesis-driven research and targeted engineering strategies for the genetic enhancement/ modification of wine yeast for commercial applications.
- ItemComparative transcriptomic and proteomic profiling of industrial wine yeast strains(2010) Rossouw, D.; Van den Dool, A. H.; Jacobson, D.; Bauer, FlorianThe geno- and phenotypic diversity of commercial Saccharomyces cerevisiae wine yeast strains provides an opportunity to apply the system-wide approaches that are reasonably well established for laboratory strains to generate insight into the functioning of complex cellular networks in industrial environments. We have previously analyzed the transcriptomes of five industrial wine yeast strains at three time points during alcoholic fermentation. Here, we extend the comparative approach to include an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis of two of the previously analyzed wine yeast strains at the same three time points during fermentation in synthetic wine must. The data show that differences in the transcriptomes of the two strains at a given time point rather accurately reflect differences in the corresponding proteomes independently of the gene ontology (GO) category, providing strong support for the biological relevance of comparative transcriptomic data sets in yeast. In line with previous observations, the alignment proves to be less accurate when assessing intrastrain changes at different time points. In this case, differences between the transcriptome and proteome appear to be strongly dependent on the GO category of the corresponding genes. The data in particular suggest that metabolic enzymes and the corresponding genes appear to be strongly correlated over time and between strains, suggesting a strong transcriptional control of such enzymes. The data also allow the generation of hypotheses regarding the molecular origin of significant differences in phenotypic traits between the two strains. Copyright © 2010, American Society for Microbiology. All Rights Reserved.
- ItemComparative transcriptomic approach to investigate differences in wine yeast physiology and metabolism during fermentation(2009) Rossouw, D.; Olivares-Hernandes, R.; Nielsen, J.; Bauer, FlorianCommercial wine yeast strains of the species Saccharomyces cerevisiae have been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level. Copyright © 2009, American Society for Microbiology. All Rights Reserved.
- ItemComparing the transcriptomes of wine yeast strains: Toward understanding the interaction between environment and transcriptome during fermentation(2009) Rossouw, D.; Bauer, FlorianSystem-wide "omics" approaches have been widely applied to study a limited number of laboratory strains of Saccharomyces cerevisiae. More recently, industrial S. cerevisiae strains have become the target of such analyses, mainly to improve our understanding of biotechnologically relevant phenotypes that cannot be adequately studied in laboratory strains. Most of these studies have investigated single strains in a single medium. This experimental layout cannot differentiate between generally relevant molecular responses and strain- or media-specific features. Here we analyzed the transcriptomes of two phenotypically diverging wine yeast strains in two different fermentation media at three stages of wine fermentation. The data show that the intersection of transcriptome datasets from fermentations using either synthetic MS300 (simulated wine must) or real grape must (Colombard) can help to delineate relevant from "noisy" changes in gene expression in response to experimental factors such as fermentation stage and strain identity. The differences in the expression profiles of strains in the different environments also provide relevant insights into the transcriptional responses toward specific compositional features of the media. The data also suggest that MS300 is a representative environment for conducting research on wine fermentation and industrially relevant properties of wine yeast strains. © 2009 Springer-Verlag.
- 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 impact of changes in environmental conditions on organic acid production by commercial wine yeast strains(South African Society for Enology and Viticulture, 2018) Chidi, B. S.; Bauer, Florian; Rossouw, D.Acidity is one of the primary sensory elements in wine, and the balance of sugar and acidity is probably the strongest element affecting wine appreciation. However, little is known about how yeast strains and fermentation conditions will affect the production of fermentation-derived acids, including acetic, succinic and pyruvic acid. This study employs a multifactorial experimental design to provide a better understanding of how individual or simultaneous changes in environmental parameters such as pH, sugar and temperature influence the production of individual organic acids during fermentation in several yeast strains in synthetic must. Certain changes in environmental factors led to conserved trends between strains and treatments. Strains produced higher succinic acid levels when temperature was increased. Significant strain-dependent differences were observed when sugar concentrations were varied for both strains: the combinatorial impact of high initial sugars and fermentation temperature was more pronounced when increased pyruvic acid production was observed in yeast strain VIN13. On the other hand, while combinatorial influences are evident, higher sugar fermentation settings were largely characterised by high acetic acid concentrations for both strains. It is clear that simultaneous changes in sugar, pH and temperature affect organic acid trends in a variable manner, depending on the particular combination of environmental parameters and yeast strain. The study provides valuable information regarding the manner in which initial must parameters and environmental conditions throughout fermentation may affect wine acidity. Since many of these parameters can be controlled at least in part during the winemaking process, the data provide important background information for oenological strategies that aim to optimise the acid balance of wines.
- 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.
- ItemOrganic acid metabolism and the impact of fermentation practices on wine acidity : a review(South African Society for Enology and Viticulture, 2018) Chidi, B. S.; Bauer, Florian; Rossouw, D.The conversion of grape sugar to ethanol and carbon dioxide is the primary biochemical reaction in alcoholic wine fermentation, but microbial interactions, as well as complex secondary metabolic reactions, are equally relevant in terms of the composition of the final wine produced. The chemical composition of a wine determines the taste, flavour and aroma of the product, and is determined by many factors such as grape variety, geographical and viticultural conditions, microbial ecology of the grapes and of the fermentation processes, and the winemaking practices. Through the years, major advances have been made in understanding the biochemistry, ecology, physiology and molecular biology of the various yeast strains involved in wine production, and how these yeasts affect wine chemistry and wine sensory properties. However, many important aspects of the impact of yeast on specific wine-relevant sensory parameters remain little understood. One of these areas of limited knowledge is the contribution of individual wine yeast strains to the total organic acid profile of wine. Wine quality is indeed very directly linked to what wine tasters frequently refer to as the sugar–acid balance. The total acidity of a wine is therefore of prime sensory importance, and acidity adjustments are a frequent and legal practice in many wineries. However, the total acidity is the result of the sum of all the individual organic acids that are present in wine. Importantly, each of these acids has its own sensory attributes, with descriptors ranging from fresh to sour to metallic. It is therefore important not only to consider total acidity, but also the contribution of each individual acid to the overall acid profile of the wine. This review will summarise the current knowledge about the origin, synthesis and analysis of organic acids in wine, as well as on the management of wine acidity.
- ItemThe effect of scale on gene expression: commercial versus laboratory wine fermentations(SPRINGER, 233 SPRING STREET, NEW YORK, USA, NY, 10013, 2012) Rossouw, D.; Jolly, N.; Jacobson, D.; Bauer, Florian
- ItemThe effect of scale on gene expression: Commercial versus laboratory wine fermentations(2012) Rossouw, D.; Jolly, N.; Jacobson, D.; Bauer, FlorianMolecular and cellular processes that are responsible for industrially relevant phenotypes of fermenting microorganisms are a central focus of biotechnological research. Such research intends to generate insights and solutions for fermentation-based industries with regards to issues such as improving product yield or the quality of the final fermentation product. For logistical reasons, and to ensure data reproducibility, such research is mostly carried out in defined or synthetic media and in small-scale fermentation vessels. Two questions are frequently raised regarding the applicability of this approach to solve problems experienced in industrial fermentations: (1) Is synthetic medium a sufficiently accurate approximation of the generally more complex natural (and frequently highly variable) substrates that are employed in most fermentation-based industries, and (2) can results obtained in small-scale laboratory fermentations be extrapolated to large-scale industrial environments? Here, we address the second question through a comparative transcriptomic approach by assessing the response of an industrial wine yeast strain fermenting a natural grape juice in small-scale laboratory and large-scale industrial conditions. In yeast, transcriptome analysis is arguably the best available tool to holistically assess the physiological state of a population and its response to changing environmental conditions. The data suggest that scale does indeed impact on some environmental parameters such as oxygen availability. However, the data show that small-scale fermentations nevertheless accurately reflect general molecular processes and adaptations during large-scale fermentation and that extrapolation of laboratory datasets to real industrial processes can be justified. © 2011 Springer-Verlag.
- ItemThe impact of co-inoculation with Oenococcus oeni on the trancriptome of Saccharomyces Cerevisiae and on the flavour-active metabolite profiles during fermentation in synthetic mus(ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD, 24-28 OVAL RD, LONDON, ENGLAND, NW17DX, 2012) Rossouw, D.; Du Toit, M.; Bauer, Florian
- ItemThe impact of co-inoculation with Oenococcus oeni on the trancriptome of Saccharomyces cerevisiae and on the flavour-active metabolite profiles during fermentation in synthetic must(2012) Rossouw, D.; Du Toit, M.; Bauer, Florian
- ItemTranscriptional regulation and the diversification of metabolism in wine yeast strains(2012) Rossouw, D.; Jacobson, D.; Bauer, FlorianTranscription factors and their binding sites have been proposed as primary targets of evolutionary adaptation because changes to single transcription factors can lead to far-reaching changes in gene expression patterns. Nevertheless, there is very little concrete evidence for such evolutionary changes. Industrial wine yeast strains, of the species Saccharomyces cerevisiae, are a geno- and phenotypically diverse group of organisms that have adapted to the ecological niches of industrial winemaking environments and have been selected to produce specific styles of wine. Variation in transcriptional regulation among wine yeast strains may be responsible for many of the observed differences and specific adaptations to different fermentative conditions in the context of commercial winemaking. We analyzed gene expression profiles of wine yeast strains to assess the impact of transcription factor expression on metabolic networks. The data provide new insights into the molecular basis of variations in gene expression in industrial strains and their consequent effects on metabolic networks important to wine fermentation. We show that the metabolic phenotype of a strain can be shifted in a relatively predictable manner by changing expression levels of individual transcription factors, opening opportunities to modify transcription networks to achieve desirable outcomes. © 2012 by the Genetics Society of America.
- ItemWine science in the omics era : the impact of systems biology on the future of wine research(SASEV, 2009) Rossouw, D.; Bauer, FlorianIndustrial wine making confronts viticulturalists, wine makers, process engineers and scientists alike with a bewildering array of independent and semi-independent parameters that can in many cases only be optimized by trial and error. Furthermore, as most parameters are outside of individual control, predictability and consistency of the end product remain difficult to achieve. The traditional wine sciences of viticulture and oenology have been accumulating data sets and generating knowledge and know-how that has resulted in a significant optimization of the vine growing and wine making processes. However, much of these processes remain based on empirical and even anecdotal evidence, and only a small part of all the interactions and cause-effect relationships between individual input and output parameters is scientifically well understood. Indeed, the complexity of the process has prevented a deeper understanding of such interactions and causal relationships. New technologies and methods in the biological and chemical sciences, combined with improved tools of multivariate data analysis, open new opportunities to assess the entire vine growing and wine making process from a more holistic perspective. This review outlines the current efforts to use the tools of systems biology in particular to better understand complex industrial processes such as wine making.