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FEMS Yeast Research May 2020Saccharomyces cerevisiae is the most extensively studied yeast and, over the last century, provided insights on the physiology, genetics, cellular biology and molecular... (Review)
Review
Saccharomyces cerevisiae is the most extensively studied yeast and, over the last century, provided insights on the physiology, genetics, cellular biology and molecular mechanisms of eukaryotes. More recently, the increase in the discovery of wild strains, species and hybrids of the genus Saccharomyces has shifted the attention towards studies on genome evolution, ecology and biogeography, with the yeast becoming a model system for population genomic studies. The genus currently comprises eight species, some of clear industrial importance, while others are confined to natural environments, such as wild forests devoid from human domestication activities. To date, numerous studies showed that some Saccharomyces species form genetically diverged populations that are structured by geography, ecology or domestication activity and that the yeast species can also hybridize readily both in natural and domesticated environments. Much emphasis is now placed on the evolutionary process that drives phenotypic diversity between species, hybrids and populations to allow adaptation to different niches. Here, we provide an update of the biodiversity, ecology and population structure of the Saccharomyces species, and recapitulate the current knowledge on the natural history of Saccharomyces genus.
Topics: Adaptation, Physiological; Ecology; Genetic Variation; Genome, Fungal; Hybridization, Genetic; Phylogeography; Saccharomyces
PubMed: 32196094
DOI: 10.1093/femsyr/foaa013 -
Current Opinion in Biotechnology Feb 2018Yeasts have been used for food and beverage fermentations for thousands of years. Today, numerous different strains are available for each specific fermentation process.... (Review)
Review
Yeasts have been used for food and beverage fermentations for thousands of years. Today, numerous different strains are available for each specific fermentation process. However, the nature and extent of the phenotypic and genetic diversity and specific adaptations to industrial niches have only begun to be elucidated recently. In Saccharomyces, domestication is most pronounced in beer strains, likely because they continuously live in their industrial niche, allowing only limited genetic admixture with wild stocks and minimal contact with natural environments. As a result, beer yeast genomes show complex patterns of domestication and divergence, making both ale (S. cerevisiae) and lager (S. pastorianus) producing strains ideal models to study domestication and, more generally, genetic mechanisms underlying swift adaptation to new niches.
Topics: Beer; Fermentation; Genetic Variation; Industrial Microbiology; Saccharomyces; Saccharomyces cerevisiae
PubMed: 28869826
DOI: 10.1016/j.copbio.2017.08.005 -
Yeast (Chichester, England) Dec 2014Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by... (Review)
Review
Yeast researchers need model systems for ecology and evolution, but the model yeast Saccharomyces cerevisiae is not ideal because its evolution has been affected by domestication. Instead, ecologists and evolutionary biologists are focusing on close relatives of S. cerevisiae, the seven species in the genus Saccharomyces. The best-studied Saccharomyces yeast, after S. cerevisiae, is S. paradoxus, an oak tree resident throughout the northern hemisphere. In addition, several more members of the genus Saccharomyces have recently been discovered. Some Saccharomyces species are only found in nature, while others include both wild and domesticated strains. Comparisons between domesticated and wild yeasts have pinpointed hybridization, introgression and high phenotypic diversity as signatures of domestication. But studies of wild Saccharomyces natural history, biogeography and ecology are only beginning. Much remains to be understood about wild yeasts' ecological interactions and life cycles in nature. We encourage researchers to continue to investigate Saccharomyces yeasts in nature, both to place S. cerevisiae biology into its ecological context and to develop the genus Saccharomyces as a model clade for ecology and evolution.
Topics: Biological Evolution; Ecosystem; Genetic Variation; Saccharomyces
PubMed: 25242436
DOI: 10.1002/yea.3040 -
FEMS Yeast Research Nov 2015Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in... (Review)
Review
Saccharomyces cerevisiae and related species, the main workhorses of wine fermentation, have been exposed to stressful conditions for millennia, potentially resulting in adaptive differentiation. As a result, wine yeasts have recently attracted considerable interest for studying the evolutionary effects of domestication. The widespread use of whole-genome sequencing during the last decade has provided new insights into the biodiversity, population structure, phylogeography and evolutionary history of wine yeasts. Comparisons between S. cerevisiae isolates from various origins have indicated that a variety of mechanisms, including heterozygosity, nucleotide and structural variations, introgressions, horizontal gene transfer and hybridization, contribute to the genetic and phenotypic diversity of S. cerevisiae. This review will summarize the current knowledge on the diversity and evolutionary history of wine yeasts, focusing on the domestication fingerprints identified in these strains.
Topics: Adaptation, Biological; Evolution, Molecular; Genetic Variation; Saccharomyces; Wine
PubMed: 26205244
DOI: 10.1093/femsyr/fov067 -
Current Opinion in Genetics &... Oct 2022Recent findings in yeast genetics and genomics have advanced our understanding of the evolutionary potential unlocked by hybridization, especially in the genus... (Review)
Review
Recent findings in yeast genetics and genomics have advanced our understanding of the evolutionary potential unlocked by hybridization, especially in the genus Saccharomyces. We now have a clearer picture of the prevalence of yeast hybrids in the environment, their ecological and evolutionary history, and the genetic mechanisms driving (and constraining) their adaptation. Here, we describe how the instability of hybrid genomes determines fitness across large evolutionary scales, highlight new hybrid strain engineering techniques, and review tools for comparative hybrid genome analysis. The recent push to take yeast research back 'into the wild' has resulted in new genomic and ecological resources. These provide an arena for quantitative genetics and allow us to investigate the architecture of complex traits and mechanisms of adaptation to rapidly changing environments. The vast genetic diversity of hybrid populations can yield insights beyond those possible with isogenic lines. Hybrids offer a limitless supply of genetic variation that can be tapped for industrial strain improvement but also, combined with experimental evolution, can be used to predict population responses to future climate change - a fundamental task for biologists.
Topics: Adaptation, Physiological; Genome; Hybridization, Genetic; Saccharomyces; Saccharomyces cerevisiae
PubMed: 35834944
DOI: 10.1016/j.gde.2022.101958 -
Microbial Biotechnology Nov 2019The dominating strains of most sugar-based natural and industrial fermentations either belong to Saccharomyces cerevisiae and Saccharomyces uvarum or are their chimeric... (Review)
Review
The dominating strains of most sugar-based natural and industrial fermentations either belong to Saccharomyces cerevisiae and Saccharomyces uvarum or are their chimeric derivatives. Osmotolerance is an essential trait of these strains for industrial applications in which typically high concentrations of sugars are used. As the ability of the cells to cope with the hyperosmotic stress is under polygenic control, significant improvement can be expected from concerted modification of the activity of multiple genes or from creating new genomes harbouring positive alleles of strains of two or more species. In this review, the application of the methods of intergeneric and interspecies hybridization to fitness improvement of strains used under high-sugar fermentation conditions is discussed. By protoplast fusion and heterospecific mating, hybrids can be obtained that outperform the parental strains in certain technological parameters including osmotolerance. Spontaneous postzygotic genome evolution during mitotic propagation (GARMi) and meiosis after the breakdown of the sterility barrier by loss of MAT heterozygosity (GARMe) can be exploited for further improvement. Both processes result in derivatives of chimeric genomes, some of which can be superior both to the parental strains and to the hybrid. Three-species hybridization represents further perspectives.
Topics: Chimera; Crosses, Genetic; Fermentation; Industrial Microbiology; Metabolic Engineering; Metabolic Networks and Pathways; Saccharomyces; Sugars
PubMed: 30838806
DOI: 10.1111/1751-7915.13390 -
Eukaryotic Cell Oct 2014Alcoholic fermentations have accompanied human civilizations throughout our history. Lager yeasts have a several-century-long tradition of providing fresh beer with... (Review)
Review
Alcoholic fermentations have accompanied human civilizations throughout our history. Lager yeasts have a several-century-long tradition of providing fresh beer with clean taste. The yeast strains used for lager beer fermentation have long been recognized as hybrids between two Saccharomyces species. We summarize the initial findings on this hybrid nature, the genomics/transcriptomics of lager yeasts, and established targets of strain improvements. Next-generation sequencing has provided fast access to yeast genomes. Its use in population genomics has uncovered many more hybridization events within Saccharomyces species, so that lager yeast hybrids are no longer the exception from the rule. These findings have led us to propose network evolution within Saccharomyces species. This "web of life" recognizes the ability of closely related species to exchange DNA and thus drain from a combined gene pool rather than be limited to a gene pool restricted by speciation. Within the domesticated lager yeasts, two groups, the Saaz and Frohberg groups, can be distinguished based on fermentation characteristics. Recent evidence suggests that these groups share an evolutionary history. We thus propose to refer to the Saaz group as Saccharomyces carlsbergensis and to the Frohberg group as Saccharomyces pastorianus based on their distinct genomes. New insight into the hybrid nature of lager yeast will provide novel directions for future strain improvement.
Topics: Beer; Biological Evolution; Chromosomes, Fungal; Fermentation; Genome, Fungal; High-Throughput Nucleotide Sequencing; Humans; Saccharomyces; Species Specificity
PubMed: 25084862
DOI: 10.1128/EC.00134-14 -
Comptes Rendus Biologies 2011Many different yeast species can take part in spontaneous fermentations, but the species of the genus Saccharomyces, including Saccharomyces cerevisiae in particular,... (Review)
Review
Many different yeast species can take part in spontaneous fermentations, but the species of the genus Saccharomyces, including Saccharomyces cerevisiae in particular, play a leading role in the production of fermented beverages and food. In recent years, the development of whole-genome scanning techniques, such as DNA chip-based analysis and high-throughput sequencing methods, has considerably increased our knowledge of fermentative Saccharomyces genomes, shedding new light on the evolutionary history of domesticated strains and the molecular mechanisms involved in their adaptation to fermentative niches. Genetic exchange frequently occurs between fermentative Saccharomyces and is an important mechanism for generating diversity and for adaptation to specific ecological niches. We review and discuss here recent advances in the genomics of Saccharomyces species and related hybrids involved in major fermentation processes.
Topics: Biological Evolution; Chromosomes, Fungal; Fermentation; Gene Dosage; Genome, Fungal; Polymorphism, Genetic; Saccharomyces; Saccharomyces cerevisiae
PubMed: 21819951
DOI: 10.1016/j.crvi.2011.05.019 -
Genetics Apr 2022Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces...
Saccharomyces cerevisiae is used to provide fundamental understanding of eukaryotic genetics, gene product function, and cellular biological processes. Saccharomyces Genome Database (SGD) has been supporting the yeast research community since 1993, serving as its de facto hub. Over the years, SGD has maintained the genetic nomenclature, chromosome maps, and functional annotation, and developed various tools and methods for analysis and curation of a variety of emerging data types. More recently, SGD and six other model organism focused knowledgebases have come together to create the Alliance of Genome Resources to develop sustainable genome information resources that promote and support the use of various model organisms to understand the genetic and genomic bases of human biology and disease. Here we describe recent activities at SGD, including the latest reference genome annotation update, the development of a curation system for mutant alleles, and new pages addressing homology across model organisms as well as the use of yeast to study human disease.
Topics: Alleles; Databases, Genetic; Genome, Fungal; Humans; Saccharomyces; Saccharomyces cerevisiae
PubMed: 34897464
DOI: 10.1093/genetics/iyab224 -
Microbial Biotechnology Aug 2022Non-wine yeasts could enhance the aroma and organoleptic profile of wines. However, compared to wine strains, they have specific intolerances to winemaking conditions....
Non-wine yeasts could enhance the aroma and organoleptic profile of wines. However, compared to wine strains, they have specific intolerances to winemaking conditions. To solve this problem, we generated intra- and interspecific hybrids using a non-GMO technique (rare-mating) in which non-wine strains of S. uvarum, S. kudriavzevii and S. cerevisiae species were crossed with a wine S. cerevisiae yeast. The hybrid that inherited the wine yeast mitochondrial showed better fermentation capacities, whereas hybrids carrying the non-wine strain mitotype reduced ethanol levels and increased glycerol, 2,3-butanediol and organic acid production. Moreover, all the hybrids produced several fruity and floral aromas compared to the wine yeast: β-phenylethyl acetate, isobutyl acetate, γ-octalactone, ethyl cinnamate in both varietal wines. Sc × Sk crosses produced three- to sixfold higher polyfunctional mercaptans, 4-mercapto-4-methylpentan-2-one (4MMP) and 3-mercaptohexanol (3MH). We proposed that the exceptional 3MH release observed in an S. cerevisiae × S. kudriavzevii hybrid was due to the cleavage of the non-volatile glutathione precursor (Glt-3MH) to detoxify the cell from the presence of methylglyoxal, a compound related to the high glycerol yield reached by this hybrid. In conclusion, hybrid generation allows us to obtain aromatically improved yeasts concerning their wine parent. In addition, they reduced ethanol and increased organic acids yields, which counteracts climate change effect on grapes.
Topics: Ethanol; Fermentation; Glycerol; Saccharomyces; Saccharomyces cerevisiae
PubMed: 35485391
DOI: 10.1111/1751-7915.14068