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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 -
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 -
Cell Metabolism Jul 2012Saccharomyces cerevisiae has directly or indirectly contributed to the identification of arguably more mammalian genes that affect aging than any other model organism.... (Review)
Review
Saccharomyces cerevisiae has directly or indirectly contributed to the identification of arguably more mammalian genes that affect aging than any other model organism. Aging in yeast is assayed primarily by measurement of replicative or chronological life span. Here, we review the genes and mechanisms implicated in these two aging model systems and key remaining issues that need to be addressed for their optimization. Because of its well-characterized genome that is remarkably amenable to genetic manipulation and high-throughput screening procedures, S. cerevisiae will continue to serve as a leading model organism for studying pathways relevant to human aging and disease.
Topics: Animals; Cell Cycle; Genes, Fungal; Humans; Longevity; Microbial Viability; Nutritional Physiological Phenomena; Oxidative Stress; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 22768836
DOI: 10.1016/j.cmet.2012.06.002 -
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 -
Current Genetics Jun 2020The translational decoding properties of tRNAs are influenced by post-transcriptional modification of nucleosides in their anticodon region. The Elongator complex... (Review)
Review
The translational decoding properties of tRNAs are influenced by post-transcriptional modification of nucleosides in their anticodon region. The Elongator complex promotes the first step in the formation of 5-methoxycarbonylmethyl (mcm), 5-methoxycarbonylhydroxymethyl (mchm), and 5-carbamoylmethyl (ncm) groups on wobble uridine residues in eukaryotic cytosolic tRNAs. Elongator mutants in yeast, worms, plants, mice, and humans not only show a tRNA modification defect, but also a diverse range of additional phenotypes. Even though the phenotypes are almost certainly caused by the reduced functionality of the hypomodified tRNAs in translation, the basis for specific phenotypes is not well understood. Here, we discuss the recent finding that the phenotypes of Saccharomyces cerevisiae Elongator mutants are modulated by the genetic background. This background-effect is largely due to the allelic variation at the SSD1 locus, which encodes an mRNA-binding protein involved in post-transcriptional regulation of gene expression. A nonsense ssd1 allele is found in several wild-type laboratory strains and the presence of this allele aggravates the stress-induced phenotypes of Elongator mutants. Moreover, other phenotypes, such as the histone acetylation and telomeric gene silencing defects, are dependent on the mutant ssd1 allele. Thus, SSD1 is a genetic modifier of the phenotypes of Elongator-deficient yeast cells.
Topics: Animals; Humans; Mice; Mutation; Peptide Chain Elongation, Translational; Phenotype; RNA Processing, Post-Transcriptional; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 31776648
DOI: 10.1007/s00294-019-01048-9 -
Current Genetics Jun 2019When faced with environmental changes, microbes enter a lag phase during which cell growth is arrested, allowing cells to adapt to the new situation. The discovery of... (Review)
Review
When faced with environmental changes, microbes enter a lag phase during which cell growth is arrested, allowing cells to adapt to the new situation. The discovery of the lag phase started the field of gene regulation and led to the unraveling of underlying mechanisms. However, the factors determining the exact duration and dynamics of the lag phase remain largely elusive. Naively, one would expect that cells adapt as quickly as possible, so they can resume growth and compete with other organisms. However, recent studies show that the lag phase can last from several hours up to several days. Moreover, some cells within the same population take much longer than others, despite being genetically identical. In addition, the lag phase duration is also influenced by the past, with recent exposure to a given environment leading to a quicker adaptation when that environment returns. Genome-wide screens in Saccharomyces cerevisiae on carbon source shifts now suggest that the length of the lag phase, the heterogeneity in lag times of individual cells, and the history-dependent behavior are not determined by the time it takes to induce a few specific genes related to uptake and metabolism of a new carbon source. Instead, a major shift in general metabolism, and in particular a switch between fermentation and respiration, is the major bottleneck that determines lag duration. This suggests that there may be a fitness trade-off between complete adaptation of a cell's metabolism to a given environment, and a short lag phase when the environment changes.
Topics: Adaptation, Physiological; Carbon; Fermentation; Gene Expression Regulation, Fungal; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 30666394
DOI: 10.1007/s00294-019-00938-2 -
Biochemistry. Biokhimiia Jul 2012The current view on phenoptosis and apoptosis as genetic programs aimed at eliminating potentially dangerous organisms and cells, respectively, is given. Special... (Review)
Review
The current view on phenoptosis and apoptosis as genetic programs aimed at eliminating potentially dangerous organisms and cells, respectively, is given. Special emphasis is placed on apoptosis (phenoptosis) in yeasts: intracellular defects and a plethora of external stimuli inducing apoptosis in yeasts; distinctive morphological and biochemical hallmarks accompanying apoptosis in yeasts; pro- and antiapoptotic factors involved in yeast apoptosis signaling; consecutive stages of apoptosis from external stimulus to the cell death; a prominent role of mitochondria and other organelles in yeast apoptosis; possible pathways for release of apoptotic factors from the intermembrane mitochondrial space into the cytosol are described. Using some concrete examples, the obvious physiological importance and expediency of altruistic death of yeast cells is shown. Poorly known aspects of yeast apoptosis and prospects for yeast apoptosis study are defined.
Topics: Apoptosis; Microbial Viability; Saccharomyces cerevisiae; Signal Transduction; Time Factors
PubMed: 22817540
DOI: 10.1134/S0006297912070097 -
Yeast (Chichester, England) Aug 2014The identification and characterization of the molecular determinants governing ageing represents the key to counteracting age-related diseases and eventually prolonging... (Review)
Review
The identification and characterization of the molecular determinants governing ageing represents the key to counteracting age-related diseases and eventually prolonging our health span. A large number of fundamental insights into the ageing process have been provided by research into the budding yeast Saccharomyces cerevisiae, which couples a wide array of technical advantages with a high degree of genetic, proteomic and mechanistic conservation. Indeed, this unicellular organism harbours regulatory pathways, such as those related to programmed cell death or nutrient signalling, that are crucial for ageing control and are reminiscent of other eukaryotes, including mammals. Here, we summarize and discuss three different paradigms of yeast ageing: replicative, chronological and colony ageing. We address their physiological relevance as well as the specific and common characteristics and regulators involved, providing an overview of the network underlying ageing in one of the most important eukaryotic model organisms.
Topics: Gene Expression Regulation, Fungal; Gene Regulatory Networks; Microbial Viability; Saccharomyces cerevisiae
PubMed: 24842537
DOI: 10.1002/yea.3020