FEMS yeast research最新文献

{"title":"Systems biology of yeast metabolism.","authors":"Jens Nielsen","doi":"10.1093/femsyr/foag026","DOIUrl":"10.1093/femsyr/foag026","url":null,"abstract":"<p><p>Metabolism underpins cellular function by supplying energy, biosynthetic precursors, and redox balance and in yeast there are thousands of metabolic reactions that are tightly coordinated through multilayered regulation. The yeast Saccharomyces cerevisiae has become a central model for studying metabolism and its regulation and following publication of its genome in 1996, this yeast became pivotal in systems biology. Systems biology integrates experimental data with mathematical modeling to analyse complex cellular networks. A major advance for metabolic analysis was the development of flux balance analysis and genome sequencing enabled reconstruction of the first genome-scale metabolic model (GEM) for yeast. This initial GEM described how hundreds of genes, reactions, and metabolites interact across compartments. Subsequent models, including Yeast8 and Yeast9, expanded the coverage and predictive power, and these models enable metabolic comparison, physiological analysis, omics integration, and design of strains that can be used for production of chemicals and biopharmaceuticals. Overall, S. cerevisiae remains a cornerstone of systems biology and biotechnology, with continued advances expected in integrative modeling and engineering 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/PMC13296557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257967","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":"Life beyond 6000 genes: from sequence to synthesis in a post-genomics era.","authors":"Roy S K Walker, Edward Archer, Paige Erpf, Ian T Paulsen, Isak S Pretorius","doi":"10.1093/femsyr/foag034","DOIUrl":"10.1093/femsyr/foag034","url":null,"abstract":"<p><p>The publication of the Saccharomyces cerevisiae genome sequence thirty years ago marked a defining shift in modern biology, establishing yeast as the first fully sequenced eukaryotic model cell. Access to a complete reference genome has catalyzed a renaissance in experimental biology, providing the foundation for advances in functional genomics, systems biology, synthetic biology, and biotechnology. This article celebrates the achievements of the yeast sequencing project and highlights how genomics has evolved from a descriptive resource into a central enabling infrastructure for engineering biology, leading to a post-genomic era defined by genome-scale design. We chart the progression from decoding the genome to the omics revolution, highlighting both recent discoveries and persistent enigmas surrounding the 'dark matter' of the yeast genome. We then describe how access to a well-annotated reference genome has culminated in a new era of synthetic genomics exemplified by the Sc2.0 project. Finally, we explore how emerging trends in artificial intelligence and bioelectronics may shape the next thirty years of yeast genomics and engineering biology. This integration of past achievements and future trajectories reinforces the enduring role of S. cerevisiae as a primary eukaryotic model for biological discovery and biotechnological innovation.</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/PMC13459950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148677788","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":"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":"10.1093/femsyr/foag040","url":null,"abstract":"<p><p>Engineering of multistep enzymatic pathways often involves extensive optimization 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 ORF libraries, which are combined and cotransformed in a one-pot method. The libraries include consensus homology arms which target long terminal repeat regions 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 of 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":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13560586/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional regulation: efficient genetic engineering tools for non-conventional yeasts.","authors":"Shabana Haneef, Yongjin J Zhou, Fan Bai","doi":"10.1093/femsyr/foag032","DOIUrl":"10.1093/femsyr/foag032","url":null,"abstract":"<p><p>Non-conventional yeasts are recognized as valuable hosts for producing biofuels, pharmaceuticals, and other high-value chemicals, owing to their diverse physiological traits, ability to utilize various substrates, and greater tolerance to environmental stresses compared to conventional model yeast Saccharomyces cerevisiae. To fully optimizing metabolic flux toward desired products, effective genetic engineering tools enabling precise modulation of gene expression and coordinated control of metabolic pathways are essential. In this context, we discussed classical transcriptional regulation tools like promoters, and transcription factors, alongside innovations in synthetic biology that allow metabolic engineering in non-conventional yeasts to produce higher biofuels and other useful products, promoting the development of sustainable resources, and assisting the development of innovative bio-products. It also discussed innovative programmable technologies, such as CRISPR/Cas-mediated transcriptional activation and repression, as well as dynamic regulatory systems that can fine-tune metabolic routes and balance cellular resources. Strategies for promoter engineering, transcription factor manipulation for transcriptional regulation, and metabolic rewiring were highlight as methods to boost pathway efficiency and yields. This review concluded with current challenges and future directions, focusing on integrating synthetic biology and systems biology to create robust, controllable transcriptional frameworks for next-generation yeast cell factories.</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/PMC13459951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668583","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":"Transcriptomic responses of kveik yeasts to heat and ethanol stress.","authors":"Daishi Shirasaya, Chris D Powell","doi":"10.1093/femsyr/foag043","DOIUrl":"10.1093/femsyr/foag043","url":null,"abstract":"<p><p>Kveik strains are a group of Saccharomyces cerevisiae strains notable for their exceptional tolerance to environmental stress. To investigate the molecular basis of this robustness, the transcriptomes of three kveik strains and a conventional ale strain were compared under non-stress and stress conditions using RNA-seq. Under non-stress conditions, kveik strains showed elevated basal expression of environmental stress response genes, suggesting that part of the stress-responsive transcriptional program is active irrespective of stress exposure. Catalase activity was elevated, providing physiological support for the transcriptomic findings related to oxidative-stress defense. Under sublethal heat stress, conventional ale yeast displayed transcriptional patterns associated with cell-cycle restraint and chromosome organization, whereas kveik strains showed enrichment of genes related to protein refolding, ribosome biogenesis, and cell-wall biosynthesis, suggesting retention of a transcriptional emphasis on growth-associated processes alongside stress-protective responses. Under ethanol stress, both groups upregulated translation-related processes; however, metabolic functions were more strongly enriched in ale yeast, while kveik strains showed patterns consistent with maintenance of translation-related functions together with increased emphasis on cell surface-associated processes. Overall, kveik stress tolerance appears to reflect elevated basal preparedness and transcriptional patterns consistent with the maintenance of biosynthetic and structural processes under stress, supporting their potential suitability for intensive industrial fermentations.</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/PMC13599773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918371","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":"Microbial ecology of fermented foods.","authors":"Anna Elizabeth Wittwer, I Nyoman Sumerta, Francesca Cristetti, Kate S Howell","doi":"10.1093/femsyr/foag050","DOIUrl":"10.1093/femsyr/foag050","url":null,"abstract":"<p><p>Over thousands of years, a wide variety of food fermentations in human diets have developed in different geographical regions, cultures, and traditions. The desirable conversions of food components that occur during fermentation rely on a diverse array of microorganisms, which interact with one another and with their environments. Notably, many yeast, bacterial, and filamentous fungal taxa are key members of the microbiomes of fermented food products. Strategies employed by these microorganisms to ensure their survival typically include maximising reproductive rates, and this affects patterns of microbial succession and key metabolic dependencies. The principles of microbial ecology can be used to understand growth, activity, and interactions in these diverse communities. In this review, we summarize the historical significance and factors influencing key microbial functions in palm wine, wine, sourdough, and tempeh, selected for their varied raw materials and fermentation techniques. Despite differences, in fermented foods abiotic and environmental influences from natural or human-controlled sources act to define a food's microbial ecology and therefore the final product's properties. Modern production of traditional and novel foods by microbes should consider the principles of microbial ecology to understand and control fermentation outcomes.</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/PMC13618444/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149012013","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":"De novo genome assembly of a native Saccharomyces cerevisiae strain isolated from spontaneous fermentation of vineyard must in the Atacama Desert (Chile).","authors":"Héctor Aguayo-Cumplido, Michelle Cifras-Céspedes, Marcelo Lanino, Ingrid Poblete, Jennifer Molinet, Lía Ramírez-Fernández","doi":"10.1093/femsyr/foag033","DOIUrl":"10.1093/femsyr/foag033","url":null,"abstract":"<p><p>In this work, we investigated the genomic and phenotypic basis of stress tolerance in the native Saccharomyces cerevisiae strain M6, isolated from spontaneously fermenting must at a vineyard located in Atacama Desert, through a de novo hybrid genome assembly generated using short- and long-read sequencing technologies. The assembly comprised 11.89 Mb with high completeness (99.5%), and flow cytometry analysis confirmed a diploid genome organization. Phylogenomic analyses placed M6 within the Wine/European lineage, although displaying genomic divergence relative to other wine-associated strains. Using S288C as the reference genome, comparative variant analysis was performed for M6 and four closely related strains, including Wine/European and Alpechin strains. Coding variants were identified in genes associated with osmotic sensing and signaling (SSK1, SSK2), trehalose metabolism (TPS2, NTH1). Growth assays demonstrate that M6 exhibits enhanced performance under elevated temperatures (35°C-38°C) and high salinity (up to 1.5 M NaCl) compared with commercial and laboratory strains. In addition, Biolog YT assays revealed broad carbohydrate utilization capacity, including the metabolism of maltose, galactose, and raffinose-family oligosaccharides. Together, these results provide integrated genomic and phenotypic evidence of stress resistance and metabolic flexibility in strain M6, highlighting its potential as a biotechnological resource for fermentation processes.</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/PMC13495792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668435","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":"Reprogramming a Hgt-family Kluyveromyces marxianus sugar transporter by site-directed mutagenesis to enable co-consumption of glucose and xylose.","authors":"Lorena Donzella, Carlos Belloch-Molina, John P Morrissey, Maria João Sousa","doi":"10.1093/femsyr/foag035","DOIUrl":"10.1093/femsyr/foag035","url":null,"abstract":"<p><p>Efficient utilization of lignocellulosic hydrolysates in yeast-based biorefineries requires simultaneous consumption of glucose and xylose, which is often limited by preferential glucose uptake. In Kluyveromyces marxianus, we kinetically characterized two native xylose transporters, KMAR_10 531 and KMAR_60 179, identifying medium- and low-affinity xylose transporters, respectively. KMAR_10 531 also mediated high-affinity glucose uptake (Km 0.28 ± 0.1 mM), limiting xylose utilization in mixed-sugar media. Guided by structural modelling, we engineered the KMAR_10 531 N325V variant, which reduced glucose affinity ∼20-fold while improving xylose affinity more than three-fold (Km reduced from 46.9 ± 9.5 to 14.9 ± 3.6 mM). Expression of KMAR_10 531 N325V in a pentose-transporter-deficient K. marxianus strain enabled simultaneous glucose-xylose co-consumption in flasks and bioreactors, overcoming the diauxic growth observed with the native transporter. In bioreactors, the engineered strain consumed ∼90% of available xylose within 45 h and produced increased biomass compared to native transporter. This study provides the first example of engineering an Hgt-like transporter for altered sugar specificity.</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/PMC13487788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148697242","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":"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":"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 30 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":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13560583/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Indigenous microorganisms and benefit sharing.","authors":"Katie Lee Riddle, Rogena Sterling, Maui Hudson, Jane Anderson","doi":"10.1093/femsyr/foag016","DOIUrl":"10.1093/femsyr/foag016","url":null,"abstract":"<p><p>This article explores the challenges and opportunities associated with benefit sharing and genetic resources in the context of microorganisms, with a particular focus on understanding Indigenous rights and perspectives. It examines traditional uses and understandings of microorganisms by Indigenous communities, evaluates existing international frameworks, and analyses case studies of emerging models of ethical engagement. It argues that benefit sharing mechanisms must be reformed to meaningfully incorporate Indigenous values, interests, and rights, particularly in respect of digital sequence information, and new or emerging biotechnologies.</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/PMC13224826/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147835666","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}