Yeast最新文献

Yeast strain development has been essential for improving efficiency, flavour diversity, and quality of beer fermentation. Such efforts often rely on laborious in vitro screening experiments. However, with the increasing availability of large-scale 'omics' data sets, it may be possible to replace or complement such experiments with in silico screening. Compared to more traditional in vitro screening, this has several benefits, including lower costs, more rapid results and possibility to include more strains. Here, we briefly review the genetics associated with various desirable and undesirable traits in brewing yeast, and demonstrate how recent genomics, transcriptomics, and proteomics data sets derived from the 1011 yeast genomes project can be exploited for identifying strains with potentially desirable phenotypes. The discussed phenotypes are related to fermentation performance, formation of desirable flavours, and mitigation of off-flavours. Finally, we perform wort fermentations with five strains from diverse backgrounds, with diverse predicted phenotypes, to validate the in silico predictions. Most predicted phenotypes correlated well with the measured phenotypes, including formation of desirable compounds like isoamyl acetate and ethyl octanoate, as well as formation of undesirable compounds like 4-vinyl guaiacol, diacetyl, and ethanethiol. Together, the results indicate that utilising large 'omics' data sets can be a very useful tool for both strain selection and development for beer fermentation, and naturally other food and beverage fermentations as well. We hope this can inspire and yield improved and more diverse brewing strains to the industry.

Biodiversity gaps in microorganisms, such as yeasts, blur our understanding of microbial diversity, introducing biases in their biogeography, ecology, and taxonomy. The genus Carlosrosaea is a potential plant growth booster, yet it is still a little-known yeast group. Considering that databases like GBIF and GenBank are powerful tools for exploring biodiversity data, we aimed to map the geographic distribution, ecological patterns, and taxonomic potential of the genus Carlosrosaea. We found 176 records of the genus, with about 70% associated with plant material, mostly leaves. Furthermore, 55% of the records pertained to the tropical region and only 12% to the temperate. The data indicates the existence of more than a dozen possible new species of the genus, cataloged yet undescribed. This study advances our understanding of the geographic, ecological, and taxonomic aspects of Carlosrosaea. It also highlights how public databases and literature reviews provide accessible ways to analyze information about microbial groups with limited data.

Meiotic recombination is a powerful source of haplotypic diversity, and thus plays an important role in the dynamics of short-term adaptation. However, high-throughput quantitative measurement of recombination parameters is challenging because of the large size of offspring to be genotyped. One of the most efficient approaches for large-scale recombination measurement is to study the segregation of fluorescent markers in gametes. Applying this to yeast spores by flow cytometry has already been proved to be highly efficient, but manual analyses of distributions of signal intensities is time-consuming and produces nonperfectly reproducible results. Such analyses are required to identify events corresponding to spores and to assign each of them to a genotypic class depending on their fluorescence intensity. The CAYSS package automatically reproduces the manual process that we've been developing to analyze yeast recombination for years, including Maximum-Likelihood estimation of fluorescence extinction (Raffoux et al. 2018a). When comparing the results of manual versus CAYSS automatic analyses of the same cytometry data, recombination rates and interference were on average very similar, with less than 3% differences on average and strong correlations (R² > 0.9). In conclusion, as compared to manual analysis, CAYSS allows to save a lot of human time and produces totally reproducible results.

Killer yeasts, such as the K1 killer strain of S. cerevisiae, express a secreted anti-competitive toxin whose production and propagation require the presence of two vertically-transmitted dsRNA viruses. In sensitive cells lacking killer virus infection, toxin binding to the cell wall results in ion pore formation, disruption of osmotic homeostasis, and cell death. However, the exact mechanism(s) of K1 toxin killing activity, how killer yeasts are immune to their own toxin, and which factors could influence adaptation and resistance to K1 toxin within formerly sensitive populations are still unknown. Here, we describe the state of knowledge about K1 killer toxin, including current models of toxin processing and killing activity, and a summary of known modifiers of K1 toxin immunity and resistance. In addition, we discuss two key signaling pathways, HOG (high osmolarity glycerol) and CWI (cell wall integrity), whose involvement in an adaptive response to K1 killer toxin in sensitive cells has been previously documented but requires further study. As both host-virus and sensitive-killer competition have been documented in killer systems like K1, further characterization of K1 killer yeasts may provide a useful model system for study of both intracellular genetic conflict and counter-adaptation between competing sensitive and killer populations.

The relationship between oral and gastric yeasts and their role in the colonization of Helicobacter pylori in the stomach was studied. Four groups of 221, 7, 44, and 10 patients were used for the isolation of H. pylori and oral and gastric yeasts. In Group 1, gastric biopsies were used for the isolation of H. pylori and yeast, rapid urease test (RUT), staining with Gram's and hematoxylin & eosin (H&E), and immunohistochemistry (IHC) methods. In the other three groups, DNAs extracted from H. pylori and yeasts were used for the amplification of H. pylori-specific genes. Wet mounts of yeasts in Group 2 were examined to observe intracellular bacteria and released EVs. Among 221 patients, 65 (29.3%) had oral yeast, 35 (15.8%) H. pylori, and 31 (14%) gastric yeast. Culture of oral yeasts showed a significant correlation with the detection of H. pylori by IHC (10.3%), Gram stain (9%), RUT (6.3%), H&E (4.9%), and culture (4%) (p < 0.05). Gram-stained biopsies showed the occurrence of yeast and H. pylori, and the release of EVs from yeast. Detection of similar H. pylori genes in oral and gastric yeasts from patients in Group 2 showed their common source. Oral yeasts in Groups 3 and 4 also carried H. pylori genes. Wet mount preparations of yeasts showed intracellular bacteria inside the yeast vacuole and the release of EVs that could carry H. pylori. Oral yeast protects its intracellular H. pylori and releases it inside EVs to safely reach gastric mucosa. Yeast, as the environmental reservoir of H. pylori, plays a crucial role in bacterial reinfection after successful eradication.

Common Saccharomyces cerevisiae lab yeast strains derived from S288C have meiotic defects and therefore are poor sporulators. Here, we developed a plasmid system containing corrected alleles of the MKT1 and RME1 genes to rescue the meiotic defects and show that standard BY4741 and BY4742 strains containing the plasmid display faster and more efficient sporulation. The plasmid, pSPObooster, can be maintained as an episome and easily cured or stably integrated into the genome at a single locus. We demonstrate the use of pSPObooster in low- and high-throughput yeast genetic manipulations and show that it can expedite both procedures without impacting strain behavior.

Saccharomyces cerevisiae is an excellent model to study the effect of external cues on cell division and stress response. 5-Fluorocuracil (5-FU) has been used to treat solid tumors since several decades. The drug was initially designed to interfere with DNA replication but was later found to exert its antiproliferative effect also via RNA-dependent processes. Since 5-FU inhibits the activity of the 3'-5'-exoribonuclease Rrp6 in yeast and mammals, earlier work has compared the effect of 5-FU treatment and RRP6 deletion at the transcriptome level in diploid synchronized yeast cells. To facilitate interpreting the expression data we have developed an improved 5-Fluorouracil RNA (5-FU^R) expression viewer. Users can access information via genome coordinates and systematic or standard names for mRNAs and Xrn1-dependent-, stable-, cryptic-, and meiotic unannotated transcripts (XUTs, SUTs, CUTs, and MUTs). Normalized log2-transformed or linear data can be displayed as filled diagrams, line graphs or color-coded heatmaps. The expression data are useful for researchers interested in processes such as cell cycle regulation, mitotic repression of meiotic genes, the effect of 5-FU treatment and Rrp6 deficiency on the transcriptome and expression profiles of sense/antisense loci that encode overlapping transcripts. The viewer is accessible at http://5fur.genouest.org.