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. 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 1,011 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 utilizing 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. Compared to more traditional in vitro screening, this has several benefits, including lower costs, more rapid results and possibility to include more strains. We hope this can inspire and yield improved and more diverse brewing strains to the industry.

Agave spirits have gained global recognition and hold a central position within the cultural heritage of Mexico. Traditional distilleries characterized by open fermentations driven by local microbial communities, persist despite the rise of industrial-scale counterparts. In this review, we explore the environmental conditions and production practices that make the must of cooked agave stems a unique habitat for colonizing microorganisms. Additionally, we review selected studies that have characterized yeast species within these communities, with a focus on their metabolic traits and genomic features. Over fifty fungal species, predominantly Saccharomycetales and few Basidiomycetes, along with a similar number of lactic and acetic acid bacteria, have been identified. Despite variations in the chemical composition of the agave substrate and diversity of cultural practices associated with each traditional fermentation process, yeast species such as Saccharomyces cerevisiae, Kluyveromyces marxianus, Torulaspora delbrueckii, and several Pichia species have been consistently isolated across all agave spirit-producing regions. Importantly, cooked agave must is rich in fermentable sugars, yet it also contains inhibitory compounds that influence the proliferation dynamics of the microbial community. We discuss some of the genetic traits that may enable yeasts to flourish in this challenging environment and how human practices may shape microbial diversity by promoting the selection of microbes that are well-adapted to agave fermentation environments. The increasing demand for agave spirits, combined with concerns about the preservation of natural resources and cultural practices associated with their production, underscores the need to deepen our understanding of all key players, including the yeast communities involved.

The Lithium-PEG method to transform yeast cells is a common experiment used by most yeast laboratories. After several optimizations, this method can yield up to 10 6 transformants / µg of plasmid. Some experiments such as library screening or complex transformation require to maximize transformation yield. Here we show that the addition of a 2M sorbitol solution acts as an osmo-protectant during and after heat shock and increases ten-fold the transformation rate. This optimization requires only one additional pipetting step compared to the initial protocol, and is therefore practical for a daily use.

We have investigated the interplay between glycolytic oscillations and intracellular K + concentration in the yeast S. cerevisiae. Intracellular K + concentration was measured using the fluorophore PBFI. We found that K + is an essential ion for the occurrence of glycolytic oscillations and that intracellular K + concentration oscillates synchronously with other variables such as NADH, intracellular ATP and mitochondrial membrane potential. We also investigated if glycolysis and intracellular K + concentration oscillate in a number of yeast strains with mutations in K + transporters in the plasma membrane, mitochondrial membrane and in the vacuolar membrane. Most of these strains are still capable of showing glycolytic oscillations, but two strains are not: (i) a strain with a deletion in the mitochondrial Mdm38p K +/H + transporter and (ii) a strain with deletion of the late endosomal Nhx1p K +/H + (Na +/H +) transporter. In these two mutant strains intracellular K + concentration seems to be low, indicating that the two transporters may be involved in transport of K + into the cytosol. In the strain Mdm38p Δ oscillations in glycolysis could be restored by addition of the K +/H + exchange ionophore nigericin. Furthermore, in two non-oscillating mutant strain with a defective V-ATPase and deletion of the Arp1p protein the intracellular K + is relatively high, suggesting that the V-ATPase is essential for transport of K + out of the cytosol and that the cytoskeleton may be involved in binding K + to reduce the concentration of free ion in the cytosol. Analyses of the time series of oscillations of NADH, ATP, mitochondrial membrane potential and potassium concentration using data-driven modeling corroborate the conjecture that K + ion is essential for the emergence of oscillations and support the experimental findings using mutant strains.

In this study, we introduce a novel approach for the high-throughput quantitative analysis of mitotic defects in the fission yeast Schizosaccharomyces pombe using Imaging Flow Cytometry (IFC). Fission yeast is a valuable model organism for cell cycle research, and the ‘cut’ phenotype, indicative of mitotic catastrophe, has been instrumental in discovering cell cycle regulators. Traditional fluorescence microscopy methods for quantifying ‘cut’ events suffer from subjectivity and limited throughput. Our IFC pipeline overcomes these limitations by automating the detection of ‘cut’ cells based on the unique characteristic of daughter cell nuclei becoming trapped in the cell wall during aberrant mitosis. We demonstrate the pipeline’s effectiveness using wild-type and mutant strains, with results validated against manual scoring. Our study establishes IFC as a powerful tool for investigating mitotic fidelity in fission yeast, with implications for advancing cell biology research.

Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing potential obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA bound regulatory factors, G-quadruplexes and RNA::DNA hybrid structures known as R-loops. Here we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled DNA repair and of systems that maintain DNA replication fork processivity and integrity. We conclude that the impacts of transcription on DNA replication by the replisome must be very mild with little direct mutagenic outcome under normal conditions. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication (BIR), which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity. By re-analysing published datasets, we show that different classes of genes have different interactions with the replisome, and that highly transcribed environment dependant genes in S. cerevisiae tend to be located close to replication origins. We have previously implicated interactions between replication origins and BIR forks in adaptive transcription-induced copy number variation events, which indicates that environment dependent genes are preferentially located in genomic environments more prone to instability, particularly under replication stress.

Atacama is the most hyper-arid Desert in the world. In this study, we describe a novel species, Nakazawaea atacamensis f. a., sp. nov., isolated from plant samples in the Atacama Desert of Chile. In total, three isolates of N. atacamensis were obtained from independent Neltuma chilensis bark samples (synonym Prosopis chilensis, Algarrobo). The novel species was delineated based on morphological, physiological, biochemical, and molecular characteristics. A neighbour-joining analysis using the sequences of the D1/D2 domains of LSU rRNA revealed that N. atacamensis sp. nov. clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3% to 5.2% in the D1/D2 domains. A phylogenomic analysis based on single nucleotide polymorphism’s data confirms that the novel species belongs to the genus Nakazawaea, and placed N. atacamensis closer to N. peltata. Phenotypic comparisons demonstrated that N. atacamensis sp. nov. exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the ATA-11A-B T strain revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5,116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of these yeasts in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375 T. The Mycobank number is MB 849680.

The yeast Saccharomyces cerevisiae and most eukaryotes carry two 5’→3’ exoribonuclease paralogues that are very similar. In yeast, they are called Xrn1, which shuttles between the nucleus and cytoplasm and executes major cytoplasmic mRNA decay, and Rat1, which carries a strong nuclear localization sequence (NLS) and localizes in the nucleus. Xrn1 is 40% homologous to Rat1 but has an extra ~500 amino acids C-terminal extension. In the cytoplasm, Xrn1 can degrade decapped mRNAs during the last round of translation by ribosomes “co-translational mRNA decay”. The division of labor between the two enzymes is still enigmatic and can serve as a paradigm for division of labor of many other paralogues. Here we show that Rat1 is capable of functioning in cytoplasmic mRNA decay, provided that Rat1 remains cytoplasmic due to its NLS disruption (cRat1). This indicates that the actual segregation of the two paralogues plays roles in their specific functions. However, segregation is not sufficient for fully complementing Xrn1 function. Specifically, cRat1 can only partially recover cell volume, mRNA stability, proliferation rate, 5’→3’ decay alterations that characterize xrn1Δ cells. In particular, co-translational decay is only little complemented by cRat1. Adding the Xrn1 C-terminal domain to Rat1 does not improve the phenotypes indicating that lack of C-terminal is not the reason for the partial complementation. Collectively, it seems that during evolution the two paralogues acquire unique features that make the division of work beneficial.

While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.

Ntšhe, a Setswana name for sweet reeds, a sweet sorghum variety ( Sorghum bicolor (L)) is a commercial crop consumed as a delicacy in enormous quantities in Botswana and in southern Africa at large. Pre and post-harvest losses due to infestation by larval stages of stem borer moths, Chilo partellus often lead to severe financial losses as consumers condemn the worm-infested sweet reeds as unpalatable, “ Mo gase ntšhe tota tota” (this is not a sweet reed). Valorisation of condemned sweet reeds is one attractive route to reduce economic losses. Here, we took advantage of our understanding of yeast-insect interactions to isolate yeasts associated with larval stages of the stem borer moths and investigated their potential for production of an alcoholic sweet reed beverage. We isolated 33 yeast strains representing from the galleries and frass as well as from the guts of the larval moths. Assessment of their ability to ferment the simplest sugar, glucose, resulted in identification of 14 strains belonging to Hanseniaspora and Candida genera. These strains were further assessed for their capacity to ferment by calculating the rate of accumulation of carbon dioxide and ethanol when grown in the principal sugars found in sweet sorghum juice as sole carbon sources as well in sweet sorghum juice. In addition, as an industrially relevant trait, we tested the potential of the strains to tolerate brewing/fermentation-associated stresses. Furthermore, we assessed the aromatic complexity of the produced beverage. Our results suggest that non-conventional yeasts associated with the larval moths have potential for valorization of condemned sweet sorghum stalks to produce a sweet sorghum beverage.