FEMS yeast research最新文献

{"title":"The Saccharomyces Genome Database - A History of Ideas and Accomplishments, 1994-2026.","authors":"J Michael Cherry, Gavin Sherlock, Stacia R Engel","doi":"10.1093/femsyr/foag042","DOIUrl":"https://doi.org/10.1093/femsyr/foag042","url":null,"abstract":"<p><p>The Saccharomyces Genome Database (SGD) is one of the longest-running and most consequential biological databases in the world. Founded in the early 1990s at Stanford University under the visionary leadership of David Botstein and developed under the long-term technical direction of J. Michael Cherry, SGD has served for more than three decades not only as the authoritative knowledge center for the budding yeast Saccharomyces cerevisiae, but also as the source for much of the fundamentals of eukaryotic biology. This history traces the arc of a remarkable intellectual and scientific project: beginning with the challenge of building the very first integrated eukaryotic genome database and evolving across thirty years into a global knowledge hub for genetics, functional genomics, and human disease research. The history is organized chronologically, with each section highlighting the central ideas, technical developments, and concrete accomplishments of that period.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148817677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simplifying Multiplex Genome Engineering in Saccharomyces cerevisiae with Intron-mediated Random Assembly and INtegration (RAIN).","authors":"Fergus S Harrison, Philip A Kelso, Alexander C Carpenter, Carmen Hawthorne, Samuel Clay, Felix Meier, Ian T Paulsen, Thomas C Williams","doi":"10.1093/femsyr/foag040","DOIUrl":"https://doi.org/10.1093/femsyr/foag040","url":null,"abstract":"<p><p>Engineering of multi-step enzymatic pathways often involves extensive optimisation of heterologous gene expression levels and requires cloning of promoter and open reading frames (ORFs) to generate expression cassettes. We present work on a nascent method for multiplex genome engineering in Saccharomyces cerevisiae that negates the requirement for cloning of expression cassettes. Our system, Random Assembly and INtegration (RAIN), uses intron-mediated homologous recombination (HR) for random in vivo assembly of exogenous promoter and open reading frame (ORF) libraries which are combined and co-transformed in a one-pot method. The libraries include consensus homology arms which target long terminal repeat regions (LTR) of the Ty1 retrotransposon, providing over a hundred possible integration loci. In this way, our developmental system aims to negate the need for in vitro combinatorial cloning of promoters and ORFs to generate expression cassettes, simplifying in vitro DNA preparation before multiplex genome engineering. This paper presents findings from a series of experiments to demonstrate a proof of concept for the RAIN system. These include: the first reported use of intron-mediated assembly of promoters and ORFs for expression of a functional gene product; up to three markerless genomic integrations; and up to five integrations with antibiotic selection. We also present a number of innovations to improve integration efficiency during multiplex engineering in S. cerevisiae including: SGS1 gene knockout; disruption of heteroduplex rejection; modified Cas9 expression architecture; and overexpression HR genes RAD52, MRE11, and RAD59. To demonstrate how our system can be used for single transformation phenotype engineering of multiple strains, we also transformed a library of methylotrophy associated genes to generate four new strains that were able to grow on a solid minimal medium with methanol as the sole additional carbon source. Our findings contribute to the ongoing efforts to improve multiplex genome engineering tools in S. cerevisiae, and provide the foundations for further development of a novel toolbox for generating useful genetic diversity for metabolic pathway engineering.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148790000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Yeasts associated with microalgal cultures in marine environments: ecological roles and biotechnological potential.","authors":"Isabel Sá-Correia, Mónica A Fernandes, Madalena Matos","doi":"10.1093/femsyr/foag002","DOIUrl":"10.1093/femsyr/foag002","url":null,"abstract":"<p><p>The large-scale cultivation of microalgae for aquaculture feed, biofuels, and high value bioproducts is often limited by microbial contamination. While bacteria have long been recognized as major algal symbionts, yeasts, though typically less abundant, are emerging as functionally significant members of the phycosphere. Yeast physiological versatility, stress tolerance, and production of bioactive metabolites enable them to exert disproportionate ecological and biotechnological influence relative to their abundance. Yeasts contribute to algal systems through metabolic complementarity, enhancing nutrient cycling, stress resilience, and culture stability. Several yeast species secrete auxins such as indole-3-acetic acid, stimulating algal cell division and photosynthetic efficiency. Biosurfactants that suppress microbial contaminants, prevent biofilm formation, and stabilize algal cultures are also produced by several yeast species. In co-cultivation systems, yeast-microalgae interactions enhance biomass, lipids, and pigment yields whilst enabling efficient use of waste substrates. Moreover, yeasts associated with microalgae are valuable producers of compounds of biotechnological relevance such as lipids, biosurfactants, pigments, enzymes, and other proteins. This review synthesizes current knowledge on yeast-microalgae associations, emphasizing their ecological relevance, functional versatility, and underexplored potential in sustainable bioprocesses and circular bioeconomy. Highlighting yeasts within algal microbiomes provides new insight into cross-kingdom cooperation and tools for developing resilient, high-performance cultivation systems.</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/PMC12878336/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146009544","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":"From discovery to application: twenty years of Meyerozyma caribbica.","authors":"Elisângela de Souza Miranda Muynarsk, Angela Alves Dos Santos, Cristina Link Rüntzel, Brigitte Sthepani Orozco Colonia, Rafaela de Oliveira Penha, Bárbara Braga Vieira Marques, Danilo Grunig Humberto da Silva, Sergio Luiz Alves","doi":"10.1093/femsyr/foag010","DOIUrl":"10.1093/femsyr/foag010","url":null,"abstract":"<p><p>Over the past two decades, Meyerozyma caribbica has been identified as a metabolically versatile and ecologically adaptable yeast with significant relevance to biotechnology, agriculture, environmental remediation, and food applications. Since its formal description in 2005, this species has demonstrated the ability to grow on a wide range of substrates and under various stress conditions, facilitating the production of valuable bioproducts such as ethanol, xylitol, arabitol, and volatile aroma compounds. Multiple strains efficiently ferment lignocellulosic hydrolysates, tolerate inhibitory compounds, and remain active at elevated temperatures, which supports their application in integrated biorefineries. In addition to its fermentative capabilities, M. caribbica serves as an effective biocontrol agent through the production of antifungal metabolites, hydrolytic enzymes, mycoparasitism, nutrient competition, and the induction of plant defense responses. Environmental functions include the degradation of dyes, hydrocarbons, and organochlorine pesticides, as well as metal biosorption and the mitigation of oxidative stress in plants. There is also increasing interest in its potential as a probiotic and as a starter culture that can modulate sensory attributes in fermented foods. This review synthesizes 20 years of research on M. caribbica, focusing on its roles in bioproduct production, plant disease management, bioremediation, and probiotic or food-related applications.</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/PMC12923170/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146164516","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":"High-throughput yeast engineering in biofoundries: towards autonomous and scalable synthetic biology.","authors":"Juan P O Martinez, Robert E Speight","doi":"10.1093/femsyr/foag003","DOIUrl":"10.1093/femsyr/foag003","url":null,"abstract":"<p><p>High-throughput yeast engineering is being transformed by biofoundries that integrate automation, artificial intelligence (AI), and standardized workflows. This review examines how these facilities accelerate strain development through the Design-Build-Test-Learn (DBTL) cycle, with advances in genome editing, phenotypic screening, and predictive modelling. It highlights Australia's involvement through the Australian Genome Foundry, Idea-BIO, and the CSIRO Biofoundiry and explores global efforts to overcome reproducibility and standardization challenges. Despite progress, key barriers remain, including protocol variability and integration of AI tools. We also highlight the opportunity for a shift toward autonomous, self-optimizing 'self-driving labs' that transition from DBTL to Design-Build-Deploy cycles. The future of yeast engineering depends not only on technological innovation, but also on the harmonization of international standards, data governance, and ethical safeguards. If fully realized, the convergence of robotics, AI, and synthetic biology will redefine yeast engineering, leading to step changes in strain performance for a variety of important products, thus enabling economic and sustainable biomanufacturing at scale.</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/PMC12927428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146051091","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":"Harnessing yeast biodiversity for advanced industrial applications.","authors":"Cheng Cheng, Yu-Zhen Li, Zhenzhi Wang, Hui Chen, Bei Liao, Kai Li, Xin-Qing Zhao","doi":"10.1093/femsyr/foag031","DOIUrl":"10.1093/femsyr/foag031","url":null,"abstract":"<p><p>Budding yeast Saccharomyces cerevisiae and various non-conventional species are widely applied in the production of diverse industrial products, including pharmaceuticals, biofuels, biochemicals, and biomaterials, due to their rich natural and engineered biodiversity. This review summarizes recent advances in harnessing yeast biodiversity for industrial applications, including natural yeast diversity derived from ecological adaptation and genetic variation across diverse environments, and artificial diversity generated through adaptive laboratory evolution, metabolic or epigenetic engineering, and synthetic biology. We highlight the establishment of strain-level culture libraries and extremophilic yeasts as models for stress adaptation. In addition, we emphasize that the integration of multi-omics analysis, AI-assisted enzyme and strain engineering, and process optimization strategies are critical for the fully exploration and utilization of yeast biodiversity for efficient bioproduction.</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/PMC13501539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148789934","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":"Mechanism of the synergistic action of oxythiamine and ketoconazole against the yeast Malassezia pachydermatis.","authors":"Magdalena Czerniecka, Adam Więcko, Adam Tylicki","doi":"10.1093/femsyr/foaf059","DOIUrl":"10.1093/femsyr/foaf059","url":null,"abstract":"<p><p>This article explains the biochemical basis of the synergistic effect of oxythiamine (OT) and ketoconazole (KTC) against Malassezia pachydermatis yeast, which was isolated from dogs exhibiting clinical signs of otitis externa. All strains were incubated on MLNA medium supplemented with OT, KTC, or a mixture of both compounds. We found that the ergosterol content was reduced by the compounds tested, both separately (20%-50%) and in combination (80%). OT alone and in combination with KTC reduced NADPH levels. However, we found no differences in acetyl-CoA levels under the influence of the compounds tested. We suggest that the synergism of OT and KTC is due to a reduction in the rate of the mevalonate pathway by inhibition of NADPH influx from the pentose phosphate pathway (transketolase inhibition by OT) and inhibition of C14-α-lanosterol demethylase by KTC. The proposed mechanism may be versatile for other yeast-like species, making the combination of OT and KTC a promising treatment option for superficial, opportunistic yeast-like infections.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12767202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145274332","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":"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":"<p><p>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.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.7,"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}

{"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":"<p><p>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.</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/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}

{"title":"Replicative age differentially predicts metabolic competence across industrial yeasts at single-cell resolution.","authors":"Marco Eigenfeld, Elisabeth Zach, Ann-Kathrin Bürkle, Benjamin Schneider, Sebastian P Schwaminger","doi":"10.1093/femsyr/foag037","DOIUrl":"10.1093/femsyr/foag037","url":null,"abstract":"<p><p>In industrial yeast fermentations, population-level viability assays routinely report healthy cultures even as aged, metabolically compromised mother-cell subpopulations go undetected. Replicative age contributes to this hidden heterogeneity, but its link to a cell's metabolic competence has been difficult to measure simultaneously in the same cell by high-throughput flow cytometry. Here, we introduce a dual-parameter flow cytometry workflow combining bud-scar labeling with a recombinant His6-SUMO-mCherry-chitin-binding domain fusion protein (∼610 nm emission) and 5(6)-carboxyfluorescein diacetate (CFDA)-based viability detection (∼525 nm), providing spectral orthogonality without computational autofluorescence correction. We applied it to four industrially relevant yeasts: Saccharomyces pastorianus W-34/70, S. cerevisiae var. diastaticus BE-134, S. cerevisiae var. chevalieri LA-01, and Komagataella phaffii X33. In S. pastorianus, viability declined monotonically from 88% in daughter cells to 5% in the oldest resolved mother-cell class; longitudinal monitoring over 96 h captured a progressive widening of the age-dependent viability gradient masked at the population level. Among S. cerevisiae variants, age-dependent gradients were weaker and strain-specific, while in K. phaffii reliable discrimination required exponential growth. Replicative age is thus a strain-dependent predictor of metabolic competence rather than a universally conserved one, and the workflow offers brewers and bioprocess developers a practical tool for age-resolved fermentation monitoring and pitching-yeast assessment.</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/PMC13499230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148688735","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}