FEMS yeast research最新文献_第2页

Uncorking wine yeast genomics from grape to glass. 揭开葡萄酒酵母基因组从葡萄到玻璃的奥秘。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag025

Dariusz R Kutyna, Sylvie Dequin, Amparo Querol, Isak S Pretorius

{"title":"Uncorking wine yeast genomics from grape to glass.","authors":"Dariusz R Kutyna, Sylvie Dequin, Amparo Querol, Isak S Pretorius","doi":"10.1093/femsyr/foag025","DOIUrl":"10.1093/femsyr/foag025","url":null,"abstract":"Unravelling the genomic blueprint of a reference laboratory strain of the yeast Saccharomyces cerevisiae 30 years ago opened a new era in understanding yeast biology. Since then, genomics has transformed our ability to study, adapt, improve, and tailor wine yeast strains in the laboratory and manage them in the cellar. This minireview highlights key advances in wine yeast genomics, from early whole-genome sequencing of industrial S. cerevisiae strains to the recent assembly of complex non-Saccharomyces genomes, including the wine spoilage yeast Brettanomyces bruxellensis. Comparative genomics has revealed the genetic foundations of strain specific traits critical to fermentation performance, aroma production, stress tolerance, and microbial interactions in the vineyard and winery. Beyond cataloguing gene content, integrative genomic approaches have elucidated evolutionary dynamics, domestication events, and adaptation to industrial environments. These insights underpin the rational development of novel starter cultures and biotechnological interventions, fostering consistent wine quality and diversity of sensory profiles for targeted consumer markets. Looking ahead, advances in pan-genomics and functional genomics promise to deepen our understanding of metabolic networks, gene-environment interactions, and the broader ecological context of wine fermentation. Collectively, the study of wine yeast genomics not only illuminates fundamental biological principles but also provides practical tools for innovation, including pathway engineering with synthetic enzyme fusions, and the creation of purpose-built synthetic neo-chromosomes. Excitingly, S. cerevisiae, the first eukaryote to have its genome sequenced, is now poised to become the first eukaryote with an entirely synthetic genome ̶ the Sc2.0 project ̶ heralding a bold future for yeast genomics.","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/PMC13281101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148156121","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}

引用次数: 0

Genomic tales of wine yeasts: from domestication to functional innovation. 葡萄酒酵母的基因组故事：从驯化到功能创新。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag039

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":"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.","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}

引用次数: 0

Mechanism of the synergistic action of oxythiamine and ketoconazole against the yeast Malassezia pachydermatis. 氧硫胺素与酮康唑协同防治厚皮马拉色菌的作用机制。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foaf059

Magdalena Czerniecka, Adam Więcko, Adam Tylicki

引用次数: 0

Prey preference and cell wall-mediated resistance shape predation efficiency in Saccharomycopsis schoenii. 舍氏酵母菌的食饵偏好和细胞壁介导的抗性决定了其捕食效率。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foaf075

Jan Ryno Smith, Rene K Naidoo-Blassoples, Florian F Bauer

{"title":"Prey preference and cell wall-mediated resistance shape predation efficiency in Saccharomycopsis schoenii.","authors":"Jan Ryno Smith, Rene K Naidoo-Blassoples, Florian F Bauer","doi":"10.1093/femsyr/foaf075","DOIUrl":"10.1093/femsyr/foaf075","url":null,"abstract":"Microbial antagonism, including predation and competition, shapes microbial community diversity and dynamics. Saccharomycopsis schoenii, a unicellular predatory yeast, serves as a distinct model for bona fide fungal predation, characterized by penetration pegs that enable predation. This study examined prey preferences of S. schoenii within wine-associated yeast consortia and assessed the role of prey adhesion and cell wall features in modulating predation efficiency. Predation assays revealed species-specific dynamics, with Saccharomyces cerevisiae showing pronounced susceptibility and Torulaspora delbrueckii displaying resistance indicative of density-dependent prey switching. Expression of prey Flo-adhesins in S. cerevisiae did not affect predation outcomes, highlighting that prey adhesion phenotypes are not primary determinants of susceptibility. In contrast, S. cerevisiae VIN13-related mutant strains with increased cell wall chitin showed variable resistance phenotypes, suggesting that chitin contributes to resistance, but that broader cell wall remodelling and structural features are relevant factors independent of chitin levels. While these findings provide a mechanistic framework for understanding predator-prey interactions and prey resistance, the ecological and evolutionary significance of these interactions remains uncertain due to the rarity of Saccharomycopsis species in natural communities. Ultimately, these results emphasize the importance of integrating laboratory and ecological perspectives to fully comprehend the evolutionary implications of fungal predatory behaviour.","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/PMC12857228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145888787","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}

引用次数: 0

From one genome to thousands, and beyond. 从一个基因组到数千个，甚至更多。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag038

Gauthier Brach, Joseph Schacherer

引用次数: 0

The macroevolution of filamentation morphology across the Saccharomycotina yeast subphylum. 酵母菌亚门纤维形态的宏观进化。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag001

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":"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.","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}

引用次数: 0

MFS-transporter Flr1 is a major drug-efflux transporter in Saccharomyces cerevisiae ascospores. mfs转运蛋白Flr1是酿酒酵母子囊孢子中主要的药物外排转运蛋白。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag011

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":"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.","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}

引用次数: 0

Combinatorial engineering approaches for improved lipid production in Saccharomyces cerevisiae. 改进酿酒酵母脂质生产的组合工程方法。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag047

Andrés Castillo, Lars Dahlgren, Xin Chen, Mauro Moreno Beltrán, Cecilia Tullberg, Verena Siewers

{"title":"Combinatorial engineering approaches for improved lipid production in Saccharomyces cerevisiae.","authors":"Andrés Castillo, Lars Dahlgren, Xin Chen, Mauro Moreno Beltrán, Cecilia Tullberg, Verena Siewers","doi":"10.1093/femsyr/foag047","DOIUrl":"10.1093/femsyr/foag047","url":null,"abstract":"Triacylglycerols (TAGs) hold substantial medical, nutritional, and industrial value. However, environmental concerns demand more sustainable production alternatives. A promising approach is the fermentation of TAG-accumulating microbes. In this study, we engineered a previously developed high-lipid producing Saccharomyces cerevisiae strain to further increase lipid accumulation through a combinatorial approach. We obtained up to 327 mg∙gCDW-1 of lipid content by deleting CKB1, encoding a subunit of casein kinase 2 (CK2) related to the regulation of lipid metabolism, in combination with the deletion of SEI1 encoding a seipin. The deletion of CKB1 combined with reduced expression of ERD1 and increased expression of YFT2, genes related to ER stability and lipid droplet production, respectively, led to 329 mg∙gCDW-1 of lipid content. Notably, in the highest lipid producer, only ERD1 and YFT2 were targeted. This strain reached up to 350 mg∙gCDW-1 of lipid content, a 41% increase in lipid accumulation. However, the strains with the highest lipid content also showed a reduction in growth rate and final biomass accumulation. The results in this study demonstrate that the outcomes of individual modifications depend on the genetic background, emphasizing the importance of identifying the appropriate combination of target genes to achieve the desired phenotype.","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/PMC13618443/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148976212","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}

引用次数: 0

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. 巴氏Starmerella batistae参考基因组的构建和Starmerella物种的注释揭示了与pombe Schizosaccharomyces pombe的意想不到的进化关系，并提出了一种替代酶法生产皂荚脂的途径。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag008

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":"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.","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}

引用次数: 0

Optimization and scale up of L-malic acid production from methanol by the methylotrophic yeast Ogataea polymorpha. 多态甲基营养酵母甲醇生产l -苹果酸的优化及规模化生产。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag017

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":"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.","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}

引用次数: 0