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Biochemistry. Biokhimiia Dec 2016Saccharomyces yeasts have been used for millennia for the production of beer, wine, bread, and other fermented products. Long-term "unconscious" selection and... (Review)
Review
Saccharomyces yeasts have been used for millennia for the production of beer, wine, bread, and other fermented products. Long-term "unconscious" selection and domestication led to the selection of hundreds of strains with desired production traits having significant phenotypic and genetic differences from their wild ancestors. This review summarizes the results of recent research in deciphering the genomes of wine Saccharomyces strains, the use of comparative genomics methods to study the mechanisms of yeast genome evolution under conditions of artificial selection, and the use of genomic and postgenomic approaches to identify the molecular nature of the important characteristics of commercial wine strains of Saccharomyces. Succinctly, data concerning metagenomics of microbial communities of grapes and wine and the dynamics of yeast and bacterial flora in the course of winemaking is provided. A separate section is devoted to an overview of the physiological, genetic, and biochemical features of sherry yeast strains used to produce biologically aged wines. The goal of the review is to convince the reader of the efficacy of new genomic and postgenomic technologies as tools for developing strategies for targeted selection and creation of new strains using "classical" and modern techniques for improving winemaking technology.
Topics: Genetic Variation; Metabolomics; Phylogeny; Proteomics; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Wine
PubMed: 28260488
DOI: 10.1134/S0006297916130046 -
International Journal of Molecular... Oct 2022The yeast has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular... (Review)
Review
The yeast has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of and humans and discuss the challenges of using as a model system.
Topics: Biological Phenomena; Biology; Cell Cycle Checkpoints; DNA Damage; Eukaryotic Cells; Humans; Saccharomyces cerevisiae
PubMed: 36232965
DOI: 10.3390/ijms231911665 -
Microbiology (Reading, England) Jan 2020
Topics: Biological Transport; Humans; Microbial Interactions; Microbiology; Periodicals as Topic; Pseudomonas; Saccharomyces cerevisiae
PubMed: 32003323
DOI: 10.1099/mic.0.000882 -
Cell Mar 2024Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural...
Cell cycle progression relies on coordinated changes in the composition and subcellular localization of the proteome. By applying two distinct convolutional neural networks on images of millions of live yeast cells, we resolved proteome-level dynamics in both concentration and localization during the cell cycle, with resolution of ∼20 subcellular localization classes. We show that a quarter of the proteome displays cell cycle periodicity, with proteins tending to be controlled either at the level of localization or concentration, but not both. Distinct levels of protein regulation are preferentially utilized for different aspects of the cell cycle, with changes in protein concentration being mostly involved in cell cycle control and changes in protein localization in the biophysical implementation of the cell cycle program. We present a resource for exploring global proteome dynamics during the cell cycle, which will aid in understanding a fundamental biological process at a systems level.
Topics: Eukaryotic Cells; Neural Networks, Computer; Proteome; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 38452761
DOI: 10.1016/j.cell.2024.02.014 -
ELife Nov 2022A new pooled screening method in yeast allows scientists to probe how protein levels are regulated by mutating thousands of genes at once.
A new pooled screening method in yeast allows scientists to probe how protein levels are regulated by mutating thousands of genes at once.
Topics: Gene Expression Regulation, Fungal; Saccharomyces cerevisiae
PubMed: 36326804
DOI: 10.7554/eLife.83907 -
Current Opinion in Chemical Biology Feb 2019Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will... (Review)
Review
Subcellular protein localisation is essential for the mechanisms that govern cellular homeostasis. The ability to understand processes leading to this phenomenon will therefore enhance our understanding of cellular function. Here we review recent developments in this field with regard to mass spectrometry, fluorescence microscopy and computational prediction methods. We highlight relative strengths and limitations of current methodologies focussing particularly on studies in the yeast Saccharomyces cerevisiae. We further present the first cell-wide spatial proteome map of S. cerevisiae, generated using hyperLOPIT, a mass spectrometry-based protein correlation profiling technique. We compare protein subcellular localisation assignments from this map, with two published fluorescence microscopy studies and show that confidence in localisation assignment is attained using multiple orthogonal methods that provide complementary data.
Topics: Mass Spectrometry; Microscopy, Fluorescence; Proteomics; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 30503867
DOI: 10.1016/j.cbpa.2018.10.026 -
FEMS Yeast Research Nov 2016The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry.... (Review)
Review
The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype-environment-phenotype relationships.
Topics: Adaptation, Biological; Metabolic Networks and Pathways; Microbial Interactions; Saccharomyces cerevisiae
PubMed: 27634775
DOI: 10.1093/femsyr/fow080 -
Briefings in Functional Genomics Mar 2016Despite a billion years of divergent evolution, the baker's yeast Saccharomyces cerevisiae has long proven to be an invaluable model organism for studying human biology.... (Review)
Review
Despite a billion years of divergent evolution, the baker's yeast Saccharomyces cerevisiae has long proven to be an invaluable model organism for studying human biology. Given its tractability and ease of genetic manipulation, along with extensive genetic conservation with humans, it is perhaps no surprise that researchers have been able to expand its utility by expressing human proteins in yeast, or by humanizing specific yeast amino acids, proteins or even entire pathways. These methods are increasingly being scaled in throughput, further enabling the detailed investigation of human biology and disease-specific variations of human genes in a simplified model organism.
Topics: Disease; Drug Discovery; Genes, Fungal; Genomics; Humans; Models, Biological; Proteins; Saccharomyces cerevisiae
PubMed: 26462863
DOI: 10.1093/bfgp/elv041 -
Brazilian Journal of Microbiology :... Jun 2021Lignocellulosic hydrolysates will also contain compounds that inhibit microbial metabolism, such as organic acids, furaldehydes, and phenolic compounds. Understanding... (Comparative Study)
Comparative Study
Lignocellulosic hydrolysates will also contain compounds that inhibit microbial metabolism, such as organic acids, furaldehydes, and phenolic compounds. Understanding the response of yeasts toward such inhibitors is important to the development of different bioprocesses. In this work, the growth capacity of 7 industrial Saccharomyces cerevisiae and 7 non-Saccharomyces yeasts was compared in the presence of 3 different concentrations of furaldehydes (furfural and 5-hydroxymetil-furfural), organic acids (acetic and formic acids), and phenolic compounds (vanillin, syringaldehyde, ferulic, and coumaric acids). Then, Candida tropicalis JA2, Meyerozyma caribbica JA9, Wickerhamomyces anomalus 740, S. cerevisiae JP1, B1.1, and G06 were selected for fermentation in presence of acetic acid, HMF, and vanillin because they proved to be most tolerant to the tested compounds, while Spathaspora sp. JA1 because its xylose consumption rate. The results obtained showed a dose-dependent response of the yeasts toward the eight different inhibitors. Among the compared yeasts, S. cerevisiae strains presented higher tolerance than non-Saccharomyces, 3 of them with the highest tolerance among all. Regarding the non-Saccharomyces yeasts, C. tropicalis JA2 and W. anomalus 740 appeared as the most tolerant, whereas Spathaspora strains appeared very sensitive to the different compounds.
Topics: Acids; Furaldehyde; Lignin; Microbial Viability; Phenols; Saccharomyces cerevisiae; Yeasts
PubMed: 33825150
DOI: 10.1007/s42770-021-00489-0 -
Cells Nov 2021In the yeast DNA replication and spindle assembly can overlap. Therefore, signaling mechanisms modulate spindle dynamics in order to ensure correct timing of chromosome... (Review)
Review
In the yeast DNA replication and spindle assembly can overlap. Therefore, signaling mechanisms modulate spindle dynamics in order to ensure correct timing of chromosome segregation relative to genome duplication, especially when replication is incomplete or the DNA becomes damaged. This review focuses on the molecular mechanisms that coordinate DNA replication and spindle dynamics, as well as on the role of spindle-dependent forces in DNA repair. Understanding the coupling between genome duplication and spindle function in yeast cells can provide important insights into similar processes operating in other eukaryotic organisms, including humans.
Topics: Anaphase; DNA Replication; Genomic Instability; Models, Biological; Saccharomyces cerevisiae; Spindle Apparatus
PubMed: 34943867
DOI: 10.3390/cells10123359