Search Results (172)

Winemaking is facing significant challenges caused by industrialization of the process, climate change, and increased consumer awareness regarding the use of chemical preservatives. Although several solutions have been proposed, the utilization of non-Saccharomyces species seems to be the most efficient one. Several non-Saccharomyces species have been employed for this purpose, with Hanseniaspora uvarum, H. vineae, Kluyveromyces marxianus, Lachancea thermotolerans, Metschnikowia pulcherrima, Pichia fermentans, P. kluyveri, Schizosaccharomyces pombe, Starmerella bacillaris, Torulaspora delbrueckii, and Wickerhamomyces anomalus being the most promising ones. However, only a restricted amount of metabolic activities can be reliably attributed to the species level, while most of them are characterized by strain variability and are also affected by the Saccharomyces cerevisiae strains used to carry out alcoholic fermentation, as well as the efficient supply of precursor molecules by the grape varieties and the conditions for their effective bioconversion. This variability necessitates the application of optimization strategies, taking into consideration all these parameters. This review article aims to assist in this direction by collecting the data referring to the winemaking practice of the most interesting non-Saccharomyces species, presenting clearly and comprehensively their most relevant features, and highlighting the effect of strain diversity. Full article

The human BUD31 gene has been associated with various processes including cancer. To better understand its function, we used genetic methods to study Schizosaccharomyces pombe cells lacking the BUD31 homologous gene (cwf14) and performed sequence analysis using bioinformatics methods. Mutant cells lacking the cwf14 gene showed cell size and division defects, altered stress response, rapamycin sensitivity, enhanced chronological aging, and increased sporulation tendency. These processes are known to be regulated by the TOR pathway. The cwf14-TOR link was also supported by further experiments. We demonstrated that most protein-coding genes affected by cwf14 deletion are upregulated, encode hydrolases, oxidoreductases, and are often involved in transport. GO enrichment drew our attention to genes related to nitrogen transport, while additional data pointed to a nutrient/nitrogen (N) sensing problem. Although Cwf14 protein is associated with spliceosome complex, most genes affected by the absence of cwf14 do not contain introns, suggesting that they are influenced indirectly by the cwf14 gene. In silico experiments have revealed that BUD31 orthologous genes are found from yeast to humans, are evolutionarily conserved with a high degree of sequence identity, conserved motifs, and structures. Since the human gene partially complemented the mutant phenotype of S. pombe cells, indicating functional homology, our data can help better understand pathological mechanisms observed in human cancer cells. Full article

NRDE2 is a highly conserved protein implicated in post-transcriptional gene silencing in Schizosaccharomyces pombe and Caenorhabditis elegans and has been shown to modulate splicing in mammals. To explore whether NRDE2 participates in additional processes in human cells, we performed tandem affinity purification followed by proteomic analysis of NRDE2 from nuclear extracts of HEK293T and HeLa cells. Our analysis confirmed the interaction of NRDE2 with its well-characterized partner, the MTR4 helicase (MTREX), as well as with multiple splicing factors. Notably, we also identified interactions with chromatin-associated proteins involved in transcription, including the Polymerase-Associated Factor 1 (PAF1) complex and elongating forms of RNA polymerase II (RNAPII). To further investigate NRDE2 function, we conducted RNA-seq following its transient depletion. Differential expression analysis revealed that loss of NRDE2 alters the expression of thousands of genes. Consistent with earlier reports, we observed splicing defects, particularly intron retention; however, our results indicate that the impact of NRDE2 on intron retention is more extensive than previously recognized. Moreover, intron retention was frequently associated with reduced mRNA expression. Together, these findings suggest that NRDE2 associates with both transcriptional and splicing machineries and plays a broader role in RNA processing than previously appreciated. Full article

Discovering new yeast species can be crucial for creating new types of beers. In this study, we investigated three new yeast species, Saccharomyces bayanus, Schizosaccharomyces japonicus and Schizosaccharomyces pombe var. malidevorans, which have not been previously used in the brewing industry. Colour, total acidity, bitterness, aroma profile, total phenolic, flavonoid, mineral content and organoleptic characteristics of beers fermented by these strains were analysed to discover their applicability in the brewing industry. They did not significantly affect the nutritional value and colour of the beers, but showed increased acidity compared to the control Saccharomyces cerevisiae. GC-MS (Gas Chromatography-Mass Spectrometry) analysis revealed 33 aroma compounds, some of which were identical and some unique. S. cerevisiae and S. bayanus produced a similar number (19–20) of aroma compounds, while S. japonicus produced the fewest, including some undesirable compounds. Isobutyl alcohol, isoamyl alcohol, acetol, dimethylpyrazine, acetic acid, 4-cyclopentene-1,3-dione, butyrolactone, 2-furanmethanol, phenylethyl alcohol, maltol and pyranone that provide desired aromas in beers could be found in every sample. The new yeasts significantly increased polyphenols and decreased flavonoid content. Based on the results above and the taste scores, the strains S. bayanus and S. pombe var. malidevorans may be suitable for brewing, while S. japonicus is less or only suitable for combined fermentation. Full article

Mitochondria possess their own genome, which encodes subunits of the electron transport chain, rendering mitochondrial protein translation essential for cellular energy metabolism. Mitochondrial dysfunction affects nuclear transcription through the retrograde response. We applied RNA-seq to investigate whether and how the inhibition of mitochondrial translation by chloramphenicol (CAP) affects transcriptome regulation in proliferating or stationary-phase cells of Schizosaccharomyces pombe growing in fermentative or respiratory media. Stationary-phase cells in glucose medium exhibited the strongest transcriptome response to CAP, characterized by expression signatures similar to those observed under other stresses, including the retrograde response. The induced genes were also significantly enriched in cytoplasmic carbon metabolism pathways, reflecting a transcriptional reprogramming from respiration to fermentation. The transcription factors Scr1 and Rst2, regulators of carbon catabolite repression (CCR), controlled a common set of carbon metabolism genes in CAP-treated stationary-phase cells, and they showed opposing effects on the lifespan of these cells. Rst2 was required for the induction of carbon metabolism genes and maintained nuclear localization in CAP-treated stationary-phase cells. A systematic genetic interaction screen revealed functional relationships of Rst2 with processes related to stress and starvation responses. These findings uncover a complex transcriptional program in stationary-phase cells that adapt to inhibited mitochondrial translation, including stress- and retrograde-like responses, contributions of the CCR factors Scr1 and Rst2, and adjustment of carbon metabolism to deal with mitochondrial dysfunction. Full article

Chromosome transmission fidelity is vital for organism fitness. Yet, extrinsic and intrinsic changes can affect this process, leading to aneuploidy, the loss/gain of chromosomes, which is a hallmark of cancer. Here, using a haploid fission yeast Schizosaccharomyces pombe strain with a segmental aneuploidy, we assayed genome stability under different temperatures and altered gene dosage. We find that S. pombe genome stability is temperature-dependent and is unexpectedly modulated by intracellular levels of inorganic polyphosphate polymers (polyP). The vtc4⁺ gene, encoding a subunit of the polyP-generating VTC complex, is present twice due to the segmental aneuploidy resulting in a gene-dosage-coupled increase in polyP. Using strains with different amounts of polyP, we find a direct negative correlation between polyP and chromosome segregation fidelity. PolyP modulates the function of the conserved CCAN kinetochore subcomplex, as the abnormal growth phenotype caused by the mutant CCAN protein Fta2-291 was rescued in the absence of polyP, while extra polyP had the opposite effect. Importantly, this appears to occur in part by modulation of the nucleolin Gar2. Gar2 is the functional homolog of the Saccharomyces cerevisiae Nsr1 protein, whose function is modulated by posttranslational polyP-mediated polyphosphorylation. Thus, polyP modulates genome stability, linking cellular metabolism to chromosome transmission fidelity. Full article

Nucleoside analogues are used as drugs and as labels in laboratory-based research. However, the effect of different nucleoside analogue mechanism(s) on cell sensitivity or mutagenesis is unclear. This is particularly important in cancer treatments where checkpoint proteins and DNA damage factors are often mutated. We tested six nucleoside analogues in fission yeast, Schizosaccharomyces pombe. We found that the mutations in the DNA replication checkpoint cause unique sensitivity profiles towards chemotherapeutic nucleoside analogues (gemcitabine, 5-fluorouracil, cytarabine) and the non-clinical analogue bromodeoxyuridine. Antiretroviral compounds, zidovudine and lamivudine, did not alter cell growth. We compared half-maximal inhibitory concentration (IC50) doses between checkpoint deficient yeast strains, examining culture growth and DNA mis-segregation. Intriguingly, gemcitabine and bromodeoxyuridine doses above the IC50 promoted better growth. Above each compound’s IC50 dose we saw that cells were insensitive to nucleoside analogue re-exposure, particularly in DNA replication checkpoint mutants (cds1∆, rad3∆). Thus, pairing nucleoside analogue use with personal genomics may inform drug choice, dose, and schedule. Finally, these data indicate that resistance may be predictable, informing clinical strategy. Full article

Dormancy is a physiological state that enables cells to survive under adverse conditions by halting their proliferation while retaining the capacity to resume growth when conditions become favorable. This remarkable transition between dormant and proliferative states occurs across a wide range of species, including bacteria, fungi, plants, and tardigrades. Among these organisms, yeast cells have emerged as powerful model systems for elucidating the molecular and biophysical principles governing dormancy and dormancy breaking. In this review, we provide a comprehensive summary of current knowledge on the molecular mechanisms underlying cellular dormancy, with particular focus on the two major model yeasts: Saccharomyces cerevisiae and Schizosaccharomyces pombe. Recent advances in multifaceted approaches—such as single-cell RNA-seq, proteomic analysis, and live-cell imaging—have revealed dynamic changes in gene expression, proteome composition, and viability. Furthermore, insights into the biophysical properties of the cytoplasm have offered new understanding of dormant cell regulation through changes in cytoplasmic fluidity. These properties contribute to both the remarkable stability of dormant cells and their capacity to exit dormancy upon environmental cues, deepening our understanding of fundamental cellular survival strategies across diverse species. Full article

Translation initiation in mitochondria involves unique mechanisms distinct from those in the cytosol or in bacteria. The Schizosaccharomyces pombe mitochondrial translation initiation factor 2 (Mti2) is the ortholog of human MTIF2, which plays a vital role in synthesizing proteins in mitochondria. Here, we investigate the insertion domain of Mti2, which stabilizes its interaction with the ribosome and is crucial for efficient translation initiation. Our results show that the insertion domain is critical for the proper folding and function of Mti2. The absence of the insertion domain disrupts cell growth and affects the expression of genes encoded by mitochondrial DNA. Additionally, we show that Mti2 physically interacts with the small subunits of mitoribosomes (mtSSU), and deletion of the insertion domain dissociates mitochondrial initiation factors from the mitoribosome, reducing the efficiency of mitochondrial translation. Altogether, these findings highlight the conserved role of the insertion domain in facilitating translation initiation in fission yeast and thus reveal shared principles of mitochondrial translation initiation in both fission yeast and humans. Full article

Background/Objectives: Codon usage bias affects gene expression and translation efficiency across species. The effective number of codons (ENC) and GC content influence codon preference, often displaying unimodal or bimodal distributions. This study investigates the correlation between ENC and GC rankings across species and how their relationship affects codon usage distributions. Methods: I analyzed nuclear-encoded genes from 17 species representing six kingdoms: one bacteria (Escherichia coli), three fungi (Saccharomyces cerevisiae, Neurospora crassa, and Schizosaccharomyces pombe), one archaea (Methanococcus aeolicus), three protists (Rickettsia hoogstraalii, Dictyostelium discoideum, and Plasmodium falciparum),), three plants (Musa acuminata, Oryza sativa, and Arabidopsis thaliana), and six animals (Anopheles gambiae, Apis mellifera, Polistes canadensis, Mus musculus, Homo sapiens, and Takifugu rubripes). Genes in all 17 species were ranked by GC content and ENC, and correlations were assessed. I examined how adding or subtracting these rankings influenced their overall distribution in a new method that I call Two-Rank Order Normalization or TRON. The equation, TRON = SUM(ABS((GC rank₁:GC rank_N) − (ENC rank₁:ENC rank_N))/(N²/3), where (GC rank₁:GC rank_N) is a rank-order series of GC rank, (ENC rank₁:ENC rank_N) is a rank-order series ENC rank, sorted by the rank-order series GC rank. The denominator of TRON, N²/3, is the normalization factor because it is the expected value of the sum of the absolute value of GC rank–ENC rank for all genes if GC rank and ENC rank are not correlated. Results: ENC and GC rankings are positively correlated (i.e., ENC increases as GC increases) in AT-rich species such as honeybees (R² = 0.60, slope = 0.78) and wasps (R² = 0.52, slope = 0.72) and negatively correlated (i.e., ENC decreases as GC increases) in GC-rich species such as humans (R² = 0.38, slope = −0.61) and rice (R² = 0.59, slope = −0.77). Second, the GC rank–ENC rank distributions change from unimodal to bimodal as GC content increases in the 17 species. Third, the GC rank+ENC rank distributions change from bimodal to unimodal as GC content increases in the 17 species. Fourth, the slopes of the correlations (GC versus ENC) in all 17 species are negatively correlated with TRON (R² = 0.98) (see Graphic Abstract). Conclusions: The correlation between ENC rank and GC rank differs among species, shaping codon usage distributions in opposite ways depending on whether a species’ nuclear-encoded genes are AT-rich or GC-rich. Understanding these patterns might provide insights into translation efficiency, epigenetics mediated by CpG DNA methylation, epitranscriptomics of RNA modifications, RNA secondary structures, evolutionary pressures, and potential applications in genetic engineering and biotechnology. Full article

The role of calcium, an essential secondary messenger, in cell division remains an outstanding question in cell biology despite several significant findings over the past few decades. Among them is the landmark discovery of intracellular calcium waves during cytokinesis, the last stage of cell division, in fish cells. Nevertheless, subsequent studies have been largely unable to determine the underlying molecular mechanism of these cytokinetic transients. At the center of this stalemate stands two challenging questions, how these calcium transients rise and what they do during cytokinesis. Yeast, despite its proven prowess as a model organism to study cell cycle, has not drawn much interest in addressing these questions. However, the recent discovery of cytokinetic calcium spikes in the fission yeast Schizosaccharomyces pombe has provided novel insights into how calcium regulates cytokinesis. In this review, I will primarily focus on our current understanding of the molecular mechanism of cytokinetic calcium transients in yeast cells. First, I will briefly recount the discovery of cytokinetic calcium transients in animal cells. This will be followed by an introduction to the intracellular calcium homeostasis. Next, I will discuss yeast cytokinetic calcium spikes, the ion channel Pkd2 that promotes these spikes, and the potential molecular targets of these spikes. I will also compare the calcium regulation of cytokinesis between yeast and animal cells. I will conclude by presenting a few critical questions in our continued quest to understand how calcium regulates cytokinesis. Full article

Background: Coronary artery bypass grafting (CABG) is one of the main treatments for coronary heart disease (CHD). Gut microbiota, including bacteria, fungi, archaea, and virus, has been reported to be associated with CHD. However, the changes in the multi-kingdom gut microbiota after CABG are not yet clear. This study aimed to explore the changes in multi-kingdom gut microbiota during the early postoperative period of CABG. Methods: We collected fecal samples from 40 patients before and 1 week after CABG surgery. Metagenomic sequencing was used to detect the microbial spectrum and gene functions in the patients’ fecal samples. Results: Post-CABG patients exhibited significant changes in the composition of multi-kingdom gut microbiota and gene functions. Among bacteria, beneficial species such as Bifidobacterium, Bacteroides, and Blautia were significantly reduced after CABG, while the harmful species Enterococcus was significantly increased. In fungi, Schizosaccharomyces pombe was significantly decreased in the postoperative group, while Saccharomyces cerevisiae and Aspergillus chevalieri were significantly increased postoperatively. Spearman correlation analysis indicated that Schizosaccharomyces pombe had positive interactions with beneficial bacteria such as Lachnospiraceae, Ruminococcus, and Blautia. Among archaea, the preoperatively enriched Methanomethylovorans-SGB40959 was significantly reduced postoperatively, and Spearman correlation analysis showed a significant positive interaction with probiotics Ruminococcus and Dorea. In viruses, the phage Enterococcus virus EFP01, which infects Enterococcus, was significantly increased postoperatively and showed a significant positive interaction with Enterococcus. Additionally, postoperative dysregulation of gene functions such as the Phosphoenolpyruvate-dependent Sugar Phosphotransferase System (PTS), Transposition, DNA-mediated, and Transposase Activity was observed, and Spearman correlation analysis indicated significant correlations between the dysregulated gene functions and the microbial communities. Conclusions: This study comprehensively revealed the changes in multi-kingdom species post-CABG. The reduction of beneficial microorganisms and the increase of harmful microorganisms after surgery are of significant clinical importance for understanding the overall health status of post-CABG patients and for optimizing postoperative treatment plans. Future research needs to further explore how to improve the prognosis of post-CABG patients by modulating the gut microbiota. Full article

The biochemistry and physiology of raw material, the metabolism of microorganisms, and the methods used for processing and storage can affect the stability of wines. Due to the antimicrobial action of sulfur dioxide and dimethyl dicarbonate, the aim of this study is to determine the optimal treatment protocol to maintain the physico–chemical and microbiological stability of white wines with high residual sugar. Thus, the present research focuses on analyzing the influence of both treatments, combined or separate, on 45 wine samples obtained from a blend of Muscat Ottonel and Fetească Regală grape varieties, where different doses of 6% aqueous SO₂ solution (40, 80, and 160 mg/L) and dimethyl bicarbonate (0, 100, and 200 mg/L) were used. In order to assess the ability of dimethyl dicarbonate to suppress microorganisms, varying concentrations of Brettanomyces bruxellensis and Schizosaccharomyces pombe yeasts were inoculated (0, 30, 100 CFU/mL wine). The results indicate that, while sulfur dioxide cannot be entirely substituted in wines, both treatments can effectively lower or inhibit the activity of spoilage microorganisms. For the wines’ physico–chemical and microbiological stability, the treatment that used the synergistic force of sulfur dioxide (160 mg/L) and dimethyl dicarbonate (200 mg/L wine) performed the best. Full article

In winemaking, malolactic fermentation (MLF), which converts L-malic acid to L-lactic acid, is often applied after the alcoholic fermentation stage to improve the sensory properties of the wine and its microbiological stability. MLF is usually performed by lactic acid bacteria, which, however, are sensitive to the conditions of alcoholic fermentation. Therefore, the development of wine yeast strains capable of both alcoholic fermentation and MLF is an important task. Using genome editing, we engineered a modified variant of the triploid wine yeast strain Saccharomyces cerevisiae I-328, in which the CAR1 arginase gene was replaced by the malate permease gene from Schizosaccharomyces pombe and the malolactic enzyme gene from Oenococcus oeni. Genome-wide transcriptional profiling confirmed the expression of the introduced genes and revealed a limited effect of the modification on global gene expression. Winemaking experiments show that genome editing did not affect fermentation activity and ethanol production, while use of the modified strain resulted in a tenfold reduction in malate content with simultaneous formation of lactate. The resulting wines had a softer and more harmonious taste compared to wine obtained using the parental strain. Inactivation of arginase, which forms urea and L-ornithine through the breakdown of arginine, also resulted in a twofold decrease in the content of urea and the carcinogenic ethyl carbamate in wine. Thus, the new strain with the replacement of the arginase gene with the MLF gene cassette is promising for use in winemaking. Full article

The development of new food processes and formulations begins at the laboratory stage, progresses through pilot plant trials, and culminates in industrial production. Although the positive effects in terms of sensory characteristics and qualitative differentiation have been widely studied at laboratory level, fermentations conducted at the industrial level by oenological Saccharomyces cerevisiae and non-Saccharomyces strains have not been thoroughly investigated. Scaling up to the industrial level is a critical process that involves more than simply increasing the dimensions of the process itself. The purpose of our research was to compare laboratory and industrial-level brewing of a novel craft beer produced with the addition of common unmalted wheat and fermented by Schizosaccharomyces pombe and S. cerevisiae strains. Fermentation was carried out using a S. cerevisiae strain either of oenological origin alone or through sequential inoculations with S. pombe. Beers produced with the mixed starter showed greater reproducibility between the two production levels than those fermented by S. cerevisiae alone. According to the results, the main differences highlighted between laboratory and industrial-level trials with S. cerevisiae alone concerned the extent of starch degradation, fermentation efficiency, and alcohol production, which were higher in brewing at the laboratory level. In contrast, beers produced at industrial level using sequential inoculation received significantly higher scores for foam quantity and persistence, as well as overall olfactory intensity, while scoring significantly lower scores for saltiness and sourness. To our knowledge, this research is the first to explore the use of Sc. pombe for industrial beer production. Full article