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763 results for “Saccharomyces”
Data from: QTL mapping of volatile compound production in Saccharomyces cerevisiae during alcoholic fermentation
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Data from: Population genomics reveals structure at the individual, host-tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland
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Heat shock improves random spore analysis in diverse strains of Saccharomyces cerevisiae
<p>Random spore analysis (RSA) is a classic method in yeast genetics that allows high-throughput purification of recombinant haploid spores following specific crosses. RSA typically involves a number of steps to induce sporulation, purge vegetative cells that fail to sporulate, and disrupt the ascus walls of sporulated cells to release haploid spores. These steps generally require expensive chemicals and/or enzymes that kill diploid cells but have few effects on spores. In the fission yeast <em>Schizosaccharomcyes pombe</em>, heat shock has been reported as an effective addition to RSA protocols, but to our knowledge heat shock not been used for this purpose in the budding yeast <em>Saccharomyces cerevisiae</em>. Here, we evaluate the effects of heat shock on vegetative and sporulated cultures of four diverse yeast strains: a European wine strain (DBVPG6765), a Japanese sake strain (Y12), a West African palm wine strain (DBVPG6044) and a North American strain isolated from the soil beneath an oak tree (YPS128). We characterize this phenotype under multiple combinations of temperature and incubation time, and find specific conditions that lead to the exclusion of vegetative cells and an enrichment in spores, which differ by strain. We also collected genome sequence data from a recombinant population that experienced multiple rounds of RSA, including one round with a heat shock treatment. These data suggest that when incorporated into an RSA protocol, heat shock leads to increased genetic diversity among the cells that survive and mate. Ultimately, our work provides evidence that short heat treatments can improve existing RSA protocols, though in a strain-specific manner. This result informs applications of high-throughput RSA protocols, such as QTL mapping and experimental evolution research.</p>
Data from: No evidence for extrinsic post-zygotic isolation in a wild Saccharomyces yeast system
Although microorganisms account for the largest fraction of Earth's biodiversity, we know little about how their reproductive barriers evolve. Sexual microorganisms such as Saccharomyces yeasts rapidly develop strong intrinsic post-zygotic isolation, but the role of extrinsic isolation in the early speciation process remains to be investigated. We measured the growth of F1 hybrids between two incipient species of Saccharomyces paradoxus to assess the presence of extrinsic post-zygotic isolation across 32 environments. More than 80% of hybrids showed either partial dominance of the best parent or over-dominance for growth, revealing no fitness defects in F1 hybrids. Extrinsic reproductive isolation therefore likely plays little role in limiting gene flow between incipient yeast species and is not a requirement for speciation.
Data from: Genome dynamics of hybrid Saccharomyces cerevisiae during vegetative and meiotic divisions
Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid showed nearly complete reduction in heterozygosity within 31 generations of meioses and improved spore viability. LOH in the meiotic lines was driven primarily by the mating of spores within the tetrad. The S288c/YJM789 hybrid lines propagated vegetatively for the same duration as the meiotic lines, showed variable LOH (from 2-3% and up to 35%). Two of the vegetative lines with extensive LOH, showed frequent and large internal LOH tracts that suggest a high frequency of recombination repair. These results suggest significant LOH can occur in the S288c/YJM789 hybrid during vegetative propagation presumably due to return to growth events. The average base substitution rates for the vegetative lines (1.82 x 10-10 per base per division) and the meiotic lines (1.22 x 10-10 per base per division), are the first genome wide mutation rate estimates for a hybrid yeast. This study therefore provides a novel context for the analysis of mutation rates (especially in the context of detecting LOH during vegetative divisions), compared to previous mutation accumulation studies in yeast that used homozygous backgrounds.
Data from: A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts
Microbes have evolved ways of interference competition to gain advantage over their ecological competitors. The use of secreted killer toxins by yeast cells through acquiring double-stranded RNA viruses is one such prominent example. Although the killer behaviour has been well studied in laboratory yeast strains, our knowledge regarding how killer viruses are spread and maintained in nature and how yeast cells co-evolve with viruses remains limited. We investigated these issues using a panel of 81 yeast populations belonging to three Saccharomyces sensu stricto species isolated from diverse ecological niches and geographic locations. We found that killer strains are rare among all three species. In contrast, killer toxin resistance is widespread in Saccharomyces paradoxus populations, but not in Saccharomyces cerevisiae or Saccharomyces eubayanus populations. Genetic analyses revealed that toxin resistance in S. paradoxus is often caused by dominant alleles that have independently evolved in different populations. Molecular typing identified one M28 and two types of M1 killer viruses in those killer strains. We further showed that killer viruses of the same type could lead to distinct killer phenotypes under different host backgrounds, suggesting co-evolution between the viruses and hosts in different populations. Taken together, our data suggest that killer viruses vary in their evolutionary histories even within closely related yeast species.
Data from: The cost of copy number in a selfish genetic element: the 2µM plasmid of Saccharomyces cerevisiae
Many autonomously replicating genetic elements exist as multiple copies within the cell. The copy number of these elements is often assumed to have important fitness consequences for both element and host, yet the forces shaping its evolution are not well understood. The 2µm is a multi-copy plasmid of Saccharomyces yeasts, encoding just four genes that are solely involved in plasmid replication. One simple model for the fitness relationship between yeasts and 2µm is that plasmid copy number evolves as a tradeoff between selection for increased vertical transmission, favoring high copy number, and selection for decreased virulence, favoring low copy number. To test this model, we experimentally manipulated the copy number of the plasmid and directly measured the fitness cost, in terms of growth rate reduction, associated with high plasmid copy number. We find that the fitness burden imposed by the 2µm increases with plasmid copy number, such that each copy imposes a fitness burden of 0.17% (±0.008%), greatly exceeding the cost expected for it to be stably maintained in yeast populations. Our results demonstrate the crucial importance of copy number in the evolution of yeast/2µm associations, and pave the way for future studies examining how selection can shape the cost of multi-copy elements.
Data from: A unique ecological niche fosters hybridization of oak-tree and vineyard isolates of Saccharomyces cerevisiae.
Differential adaptation to distinct niches can restrict gene flow and promote population differentiation within a species. However, in some cases the distinction between niches can collapse, forming a hybrid niche with features of both environments. We previously reported that distinctions between vineyards and oak soil present an ecological barrier that restricts gene flow between lineages of Saccharomyces cerevisiae. Vineyard isolates are tolerant to stresses associated with grapes while North American oak strains are particularly tolerant to freeze-thaw cycles. Here, we report the isolation of Saccharomyces cerevisiae strains from Wisconsin cherry trees, which display features common to vineyards (e.g. high sugar concentrations) and frequent freeze-thaw cycles. Genome sequencing revealed that the isolated strains are highly heterozygous and represent recent hybrids of the oak x vineyard lineages. We found that the hybrid strains are phenotypically similar to vineyard strains for some traits, but are more similar to oak strains for other traits. The cherry strains were exceptionally good at growing in cherry juice, raising the possibility that they have adapted to this niche. We performed transcriptome profiling in cherry, oak, and vineyard strains and show that the cherry-tree hybrids display vineyard-like or oak-like expression, depending on the gene sets, and in some cases the expression patterns linked back to shared stress tolerances. Allele-specific expression in these natural hybrids suggested concerted cis-regulatory evolution at sets of functionally regulated genes. Our results raise the possibility that hybridization of the two lineages provides a genetic solution to the thriving in this unique niche.
Data from: Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains
Natural selection has the potential to act on all phenotypes, including genomic mutation rate. Classic evolutionary theory predicts that in asexual populations, mutator alleles, which cause high mutation rates, can fix due to linkage with beneficial mutations. This phenomenon has been demonstrated experimentally and may explain the frequency of mutators found in bacterial pathogens. By contrast, in sexual populations, recombination decouples mutator alleles from beneficial mutations, preventing mutator fixation. In the facultatively sexual yeast Saccharomyces cerevisiae, segregating alleles of MLH1 and PMS1 have been shown to be incompatible, causing a high mutation rate when combined. These alleles had never been found together naturally, but were recently discovered in a cluster of clinical isolates. Here we report that the incompatible mutator allele combination only marginally elevates mutation rate in these clinical strains. Genomic and phylogenetic analyses provide no evidence of a historically elevated mutation rate. We conclude that the effect of the mutator alleles is dampened by background genetic modifiers. Thus, the relationship between mutation rate and microbial pathogenicity may be more complex than once thought. Our findings provide rare observational evidence that supports evolutionary theory suggesting that sexual organisms are unlikely to harbour alleles that increase their genomic mutation rate.
Whole genome sequencing data for Saccharomyces cerevisiae CBS 493.94
<p>SNP distance matrix.</p>
Supplementary material 1 from: Marinovska PG, Todorova TI, Boyadzhiev KP, Pisareva EI, Tomova AA, Parvanova PN, Dimitrova M, Chankova SG, Petrova VY (2022) Cellular susceptibility and oxidative stress response to menadione of logarithmic, quiescent, and nonquiescent Saccharomyces cerevisiae cell populations. In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 127-138. https://doi.org/10.3897/biorisk.17.77320
Figure S1
Ensembl r88 Saccharomyces Cerevisia LinkSets
<p>Ensembl Saccharomyces Cerevisia LinkSets</p> <p>Gene - Transcript - Protein</p>
Figure 4 in EVALUATION OF THE EFFECTIVENESS OF USING A UNIVERSAL METHOD FOR ISOLATING GENOMIC dsDNA BY SALTING OUT TECHNIQUE ACCORDING TO THE S.M. ALJANABI AND I. MARTINEZ PROTOCOL FOR YEAST SACCHAROMYCES CEREVISIAE
Figure 4. Visualisation of isolated yeast DNA (Saccharomyces cerevisiae) using the S.M. Aljanabi and I. Martinez universal protocol in 1.8% Agarose gel by horizontal electrophoresis. DNA size marker/Ladder: Gene Ruler 100bp. Plus DNA Ladder (Thermo Scientific).
Figure 2 in Saccharomyces cerevisiae OS303 expression of an alkaline protease from a newly isolated Bacillus subtilis D9
Figure 2. Analysis cloning vector construction containing alkaline protease gene with restriction enzymes to confirm the integrity of the PCR product of alkaline protease gene and to design the appropriate primers to construct the expression vector. By the enzyme combination of NheI- NdeI- BamHI restriction enzymes showed two bands of approximately 3000bp and ~1300bp must be shown as alkaline protease gene. Lane 1: DNA size marker hyperladder I; Lane 2, 3, 4, and 5: Digested sample of TA Cloning vector construction containing alkaline protease with enzyme SpeI, EcoRI, XbaI, and NheI- NdeI- BamHI respectively.
Figure 3 in Saccharomyces cerevisiae OS303 expression of an alkaline protease from a newly isolated Bacillus subtilis D9
Figure 3. Analysis of expression cloning vector (digested and purified cloning vector pRS426/GAL1p-207-Glu-MS ligated with alkaline protease called in this study pRS426/GAL1p-207-Glu-MS/ alkaline-protease plasmids. To screen the recombinant plasmids, the plasmids prepared from colonies were digested with double restriction enzymes and then were run on 0.8% agarose gel electrophoresis. Lane 1: DNA size marker hyperladder I; Lane 2, 3: pRS426/GAL1p-207-Glu-MS/alkaline-protease plasmid digested with BamHI and SpeI, after digestion, two bands of>6000bp and <1500bp observed.
Data from: Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution.
Most laboratory evolution studies that characterize evolutionary adaptation genomically focus on genetically simple traits that can be altered by one or few mutations. Such traits are important, but they are few compared with complex, polygenic traits influenced by many genes. We know much less about complex traits, and about the changes that occur in the genome and in gene expression during their evolutionary adaptation. Salt stress tolerance is such a trait. It is especially attractive for evolutionary studies, because the physiological response to salt stress is well-characterized on the molecular and transcriptome level. This provides a unique opportunity to compare evolutionary adaptation and physiological adaptation to salt stress. The yeast Saccharomyces cerevisiae is a good model system to study salt stress tolerance, because it contains several highly conserved pathways that mediate the salt stress response. We evolved three replicate lines of yeast under continuous salt (NaCl) stress for 300 generations. All three lines evolved faster growth rate in high salt conditions than their ancestor. In these lines, we studied gene expression changes through microarray analysis and genetic changes through next generation population sequencing. We found two principal kinds of gene expression changes, changes in basal expression (82 genes) and changes in regulation (62 genes). The genes that change their expression involve several well-known physiological stress-response genes, including CTT1, MSN4 and HLR1. Next generation sequencing revealed only one high-frequency single-nucleotide change, in the gene MOT2, that caused increased fitness when introduced into the ancestral strain. Analysis of DNA content per cell revealed ploidy increases in all the three lines. Our observations suggest that evolutionary adaptation of yeast to salt stress is associated with genome size increase and modest expression changes in several genes.
Treatment of Patients With Human Immunodeficiency Virus (HIV)-Related Chronic Diarrhea With Saccharomyces Boulardii or Placebo: A Double Blind Trial
ClinicalTrials.gov study NCT00002088. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains
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Data from: Tempo and mode of multicellular adaptation in experimentally evolved Saccharomyces cerevisiae
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Data from: A population study of killer viruses reveals different evolutionary histories of two closely related Saccharomyces sensu stricto yeasts
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