{"title":"From one genome to thousands, and beyond.","authors":"Gauthier Brach, Joseph Schacherer","doi":"10.1093/femsyr/foag038","DOIUrl":"10.1093/femsyr/foag038","url":null,"abstract":"<p><p>Over the past three decades, Saccharomyces cerevisiae has gone from being the first eukaryote to have its genome fully sequenced to one of the most studied biological systems. Advances in sequencing technologies, functional genomics, and population genomics have expanded the scope of study from a single laboratory reference genome to thousands of natural isolates, and the species-wide pangenome. These advances have revealed vast genetic and structural diversity, shaped by evolution, ecology, and domestication, while large-scale experimental resources have made yeast a model organism of choice in systems biology. In this review, we trace this transition from a reference genome view to an understanding of diversity at the population level, highlighting how telomere-to-telomere assemblies, graph-pangenome, and multi-omics approaches are transforming our ability to link genomic variation to phenotype. Together, these advances place S. cerevisiae at the forefront of efforts to understand and predict genotype-phenotype relationships in eukaryotes.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13501540/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148701130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Carmen Becerra-Rodríguez, Hugo Devillers, Jean-Luc Legras, Virginie Galeote, Frédéric Bigey, Sylvie Dequin, Souhir Marsit
{"title":"Genomic tales of wine yeasts: from domestication to functional innovation.","authors":"Carmen Becerra-Rodríguez, Hugo Devillers, Jean-Luc Legras, Virginie Galeote, Frédéric Bigey, Sylvie Dequin, Souhir Marsit","doi":"10.1093/femsyr/foag039","DOIUrl":"10.1093/femsyr/foag039","url":null,"abstract":"<p><p>Over the last decades, the yeast Saccharomyces cerevisiae has emerged as a key model for studying microbial domestication, particularly in the context of winemaking. The recent surge of population genomic data, encompassing thousands of genomes, has profoundly reshaped our understanding of the evolutionary history and adaptive potential of wine yeasts. Despite arising from a domestication bottleneck, wine yeasts form a well-structured population and display striking genome dynamism. Extensive variation in heterozygosity, aneuploidy, structural variations, and gene content may provide a reservoir of genomic variation that contributes to adaptive potential in the harsh winemaking environment. While some genetic variation and genome restructuring contribute to adaptation, gene flow through hybridization, introgression and especially horizontal gene transfer has emerged as a major driver of functional innovation. These findings establish wine yeasts as a powerful model to link genome evolution with adaptation to anthropogenic environments. They also provide a foundation for the rational improvement of industrial strains through approaches such as quantitative trait locus mapping, adaptive laboratory evolution and genome-wide association studies. Extending these frameworks to non-Saccharomyces species and integrating genomic, functional and ecological data will be key to understanding and engineering microbial communities, to face the modern winemaking challenges.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13525634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148789945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Arina M Adamovich, Dmitry A Knorre, Kseniia V Galkina
{"title":"MFS-transporter Flr1 is a major drug-efflux transporter in Saccharomyces cerevisiae ascospores.","authors":"Arina M Adamovich, Dmitry A Knorre, Kseniia V Galkina","doi":"10.1093/femsyr/foag011","DOIUrl":"10.1093/femsyr/foag011","url":null,"abstract":"<p><p>In fungi, spores represent a highly resilient stage of the life cycle, characterized by low metabolic activity that confers resistance to xenobiotics. However, as soon as spores start germination, they become vulnerable to low-molecular-weight toxins. We hypothesized that during sporulation fungi presynthesize spore-specific drug-efflux transporters to mitigate this vulnerability. To test this hypothesis, we compared the repertoire of ATP-binding cassette- and major facilitator superfamily (MFS)- transporters involved in multidrug resistance (MDR) between spores and proliferating cells of yeast Saccharomyces cerevisiae. Using a set of strains in which MDR-transporters are tagged with a GFP, we showed that in spores the major efflux pump is MFS transporter Flr1, whereas in proliferating vegetative cells it is Pdr5p. In the presence of xenobiotics, deletion of the FLR1 gene reduced the growth rate of microcolonies originating from spores but did not affect growth from vegetative cells. We propose that Pdr5p's basal ATPase activity may be disadvantageous for spores, as it could be detrimental during prolonged dormancy.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12974944/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146212793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christina M Chavez, Marie-Claire Harrison, Thodoris Danis, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas
{"title":"The macroevolution of filamentation morphology across the Saccharomycotina yeast subphylum.","authors":"Christina M Chavez, Marie-Claire Harrison, Thodoris Danis, Marizeth Groenewald, Chris Todd Hittinger, Antonis Rokas","doi":"10.1093/femsyr/foag001","DOIUrl":"10.1093/femsyr/foag001","url":null,"abstract":"<p><p>Saccharomycotina is a subphylum of ascomycete fungi with diverse asexual growth morphologies. Filamentous growth can comprise linear and branched budding cells that do not undergo cell separation, termed pseudohyphae, or tubular filaments with septa that perforate allowing movement of organelles, termed true hyphae. We integrated phenotypic, genomic, metabolic, and environmental data on isolation sources from 1051 species to examine the variation and evolutionary history of filamentation across Saccharomycotina and determine whether these data could predict filamentation types. We found that 63.37% of strains can form filaments; 6.56% true hyphae, 42.40% pseudohyphae, and 14.39% both true hyphae and pseudohyphae. The distributions of species that can produce true hyphae or filament were more strongly correlated with the yeast phylogeny than the distribution of species with pseudohyphae. Ancestral state reconstruction suggested that true hyphal and pseudohyphal morphologies evolved several times, that most yeast ancestors likely produced pseudohyphae or lacked filaments, and that the Saccharomycotina last common ancestor likely produced pseudohyphae but not true hyphae. Machine learning models trained on genomic and metabolic features predicted filament morphologies with ∼70% accuracy. Connecting the evolution of morphologies to their genomic, physiological, and ecological characteristics will enrich our understanding of how the diversity of lifestyles evolved in Saccharomycotina.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12878333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145997699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Soukaina Timouma, Alistair Hanak, Laura Natalia Balarezo Cisneros, Ian Donaldson, Fernando Valle, Daniela Delneri
{"title":"Construction of a reference genome for Starmerella batistae and annotation of Starmerella species reveal an unexpected evolutionary relationship with Schizosaccharomyces pombe and suggest an alternative enzymatic route for sophorolipid production.","authors":"Soukaina Timouma, Alistair Hanak, Laura Natalia Balarezo Cisneros, Ian Donaldson, Fernando Valle, Daniela Delneri","doi":"10.1093/femsyr/foag008","DOIUrl":"10.1093/femsyr/foag008","url":null,"abstract":"<p><p>The Starmerella clade is known for displaying osmotolerant and acidophilic traits from their association with bees. Several species in this genus can produce sophorolipids, which are commercially produced as biosurfactants. Here, we isolated a yeast contaminant from the laboratory environment, identified as Starmerella batistae, able to thrive at low pH and relative high temperatures. We sequenced and conducted a de novo genome assembly in three chromosomes and a mitochondrial genome for S. batistae (ca. 9.3 Mb). Based on this reference genome we functionally annotated 29 Starmerella species, using the publicly available sequences. Phylogenetic analysis across different yeast clades revealed a close relationship between Starmerella and Schizosaccharomyces yeasts. Fifteen genes were uniquely shared between Schizosaccharomyces pombe and S. batistae, of which twelve were involved in cell morphology, reflecting the fact that S. batistae cells are elongated rather than round. We found that all the Starmerella sophorolipid-producing strains shared a close common ancestor. One-to-one orthologs of Starmerella bombicola sophorolipid pathway were only found in S. kuoi (full pathway, but inverted), and in S. powellii and S. floricola (partial pathway). These findings support the notion that alternative pathways for the production of sophorolipids have evolved in different Starmerella lineages.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12983215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146118264","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Modelling human proteostasis and organelle homeostasis disorders in yeast and its application in drug discovery.","authors":"Anh V Do, Memoona Zahra, Alan L Munn","doi":"10.1093/femsyr/foag023","DOIUrl":"10.1093/femsyr/foag023","url":null,"abstract":"<p><p>Disruptions in cellular homeostasis and proteostasis are central to many human diseases, yet direct mechanistic investigation in human systems remains constrained by biological complexity and ethical limitations. Therefore, researchers have turned to the use of model systems that allow the more efficient dissection of fundamental cellular processes. The unicellular yeast Saccharomyces cerevisiae has emerged as a powerful eukaryotic model for studying disorders driven by defects in homeostasis and proteostasis. The relevant processes are highly conserved in yeast, enabling precise genetic manipulation and real-time analysis of mechanisms that are difficult to study in mammalian systems. Yeast models have been deployed to study prion propagation, lysosomal enzyme trafficking, and mitochondrial dysfunction. Yeast also provides a versatile platform for drug discovery, particularly through the use of the yeast two-hybrid system and high-throughput screens. Despite an inability to recapitulate the full complexity of multicellular organisms, yeast remains an invaluable tool for investigating human diseases and for the development of therapeutics. This review highlights how yeast has uniquely advanced the understanding of human diseases including those associated with prions, lysosomal proteins, and mitochondria and can be combined with the utility of yeast in drug discovery-collectively establishing yeast as a model for studying human disorders.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13263897/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148143250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alessandra Mauri, Miroslava Yovcheva, Philipp Demling, Eva Miriam Buhl, Hendrik Ballerstedt, Lars M Blank
{"title":"Optimization and scale up of L-malic acid production from methanol by the methylotrophic yeast Ogataea polymorpha.","authors":"Alessandra Mauri, Miroslava Yovcheva, Philipp Demling, Eva Miriam Buhl, Hendrik Ballerstedt, Lars M Blank","doi":"10.1093/femsyr/foag017","DOIUrl":"10.1093/femsyr/foag017","url":null,"abstract":"<p><p>Industrial production of malic acid remains dependent on fossil resources or, when performed microbiologically, on sugar-based feedstocks. Both routes come with caveats, generating emissions and competing with food supply. The use of CO₂-derived one-carbon substrates offers a promising alternative to circumvent these constraints. In this study, the malic acid production process from methanol in metabolically engineered Ogataea polymorpha NYCY495 LEU-ΔSTE12 Pyc Mdh MAE1 strain was optimized and scaled up. A two-phase cultivation strategy, using glycerol for biomass formation and methanol for product synthesis, was established in shake flasks and subsequently transferred to a 1 L bioreactor. Process optimization through automated feeding strategies was evaluated. DO-based feeding was the most effective approach, using a combination of methanol and glycerol, achieving a final molar yield of 0.1 molMA molMeOH ⁻¹ and a maximum productivity of 0.5 g l⁻¹ h⁻¹. This successful fermentation strategy was validated using green methanol, showcasing the feasibility of \"closing the loop\" as envisioned in the bioeconomy. Finally, a comparative study of the effect of glycerol, methanol, and their mixture on O. polymorpha NYCY495 LEU-ΔSTE12 Pyc Mdh MAE1 methanol metabolism, peroxisome biogenesis, and cellular redox balance is presented, supporting the positive cumulative effect of both on gene transcription.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13189001/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147812832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yi-Ching Lee, Chi-Chun Huang, Matilda McDaniel, Su-Ju Lin
{"title":"The nicotinamide mononucleotide adenylyl transferase (NMNAT/Nma1) modulates phosphate-sensing (PHO) signaling independent of its NAD+ synthesis activity in Saccharomyces cerevisiae.","authors":"Yi-Ching Lee, Chi-Chun Huang, Matilda McDaniel, Su-Ju Lin","doi":"10.1093/femsyr/foag041","DOIUrl":"10.1093/femsyr/foag041","url":null,"abstract":"<p><p>Regulation of NAD+ metabolism is interconnected with multiple nutrient-sensing pathways and cellular processes. The phosphate (Pi)-sensing (PHO) signaling pathway contributes to NAD+ degradation, and PHO-responsive genes are reciprocally regulated in a NAD+-dependent manner. In this study, we examine whether the NAD+ biosynthetic enzyme Nma1 has a direct role in modulating PHO signaling. We show that Nma1 physically interacts with Pho4, a transcription factor translocating to the nucleus to activate PHO-responsive genes during Pi depletion. Overexpression of NMA1 or its catalytically inactive variant significantly reduces Pi depletion-induced Pho4 nuclear localization and the activation of PHO-responsive genes, indicating the NAD+ synthesis activity of Nma1 is dispensable in the downregulation of PHO signaling. Interestingly, mutating the C-terminal domain of Nma1, which is required for the ATPase chaperone activity of mammalian NMNATs, fails to decrease Pho4 nuclear localization and the expression of PHO-responsive genes. Moreover, loss of Nma1 increases Pho4 nuclear localization under moderate Pi-depleted conditions, suggesting that cells lacking Nma1 are more sensitive to Pi availability alterations. These results support that Nma1 can moderate PHO activation by maintaining Pho4 in the cytoplasm. Our findings uncover a novel regulatory mechanism for PHO signaling, and this regulation may help coordinate NAD+ metabolism with Pi homeostasis.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13519963/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148789982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Thiol groups are determinant for overcoming acetic acid and pH stress in wine and beer fermentation-derived Saccharomyces cerevisiae strains.","authors":"Anahit Shirvanyan, Angela Primavera, Nicoletta Guaragnella, Rodrigo Ledesma-Amaro, Karen Trchounian","doi":"10.1093/femsyr/foag004","DOIUrl":"10.1093/femsyr/foag004","url":null,"abstract":"<p><p>Acetic acid (AA), a natural by-product of ethanol fermentation in yeast cells, is widely present in lignocellulosic hydrolysate as a fermentation inhibitor. Thus, gaining insight into the molecular mechanisms of AA tolerance in yeast is particularly relevant for industrial applications. This study investigates the response to AA stress in two Saccharomyces cerevisiae strains (ATCC 9804 and ATCC 13007) during different metabolic states (fermentation, respiro-fermentation, and respiration) and external pH levels (3․0 and 4.5). The results show that AA reduces the viability of both strains in a dosage-dependent manner. Moreover, ATCC 13007 is more sensitive to AA stress compared to ATCC 9804. Respiratory metabolism and higher pH correlate with better resistance to AA stress. Catalase activity was observed to increase by 1.5-6-fold under AA stress conditions, in accordance with changes in yeast thiol group content and growth. The influence of AA stress is reactive oxygen species-dependent, and redox balance regulation was found to increase the robustness of S. cerevisiae ATCC 13007 to AA by 2-fold. The study reveals valuable insights into yeast adaptation to stress conditions, contributing to the development of robust yeast strain construction for high-yield biomass and chemicals production.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12884846/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146085172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ronald Alexander Marr, Pablo Cartes, Brendan Cook, Vivien Measday
{"title":"Evaluating Canadian yeast strains for novel new-make spirit applications.","authors":"Ronald Alexander Marr, Pablo Cartes, Brendan Cook, Vivien Measday","doi":"10.1093/femsyr/foag005","DOIUrl":"10.1093/femsyr/foag005","url":null,"abstract":"<p><p>Whisky is an alcoholic beverage derived from fermented grain mash that is distilled into 'new make spirit' before maturing in barrels. While most research on whisky innovation has focused on raw materials or maturation, yeast strain selection remains a relatively underexplored avenue for product diversification. Here, we evaluated yeast diversity for whisky production by screening 110 strains sourced from Canadian vineyards for maltose utilization followed by assessing 29 candidate strains in malt extract fermentations. Seven strains representing distinct genetic backgrounds were advanced to pilot-scale fermentations, including a commercial whisky control strain of Saccharomyces cerevisiae, four other S. cerevisiae strains, one Torulaspora delbrueckii strain, and one Saccharomyces uvarum strain isolated from British Columbia wine fermentations. Fermentation performance was assessed via high performance liquid chromatography, and volatile organic compounds in new make spirits were profiled using headspace solid-phase microextraction-gas chromatography-mass spectrometry. All strains completed fermentation except T. delbrueckii, despite undergoing sequential inoculation with a commercial whisky strain. Fermentations with non-S. cerevisiae yeast strains contained elevated levels of glycerol and organic acids. Volatile organic compounds analysis identified 43 compounds, revealing strain-dependent aroma diversity. Notably, S. uvarum P01E08 was enriched in 2-phenylethyl octanoate, phenylethyl alcohol, and phenylethyl acetate. These findings highlight diverse regional yeast selection as a viable strategy to expand whisky sensory diversity.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12884848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146092487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}