Matías Guerrero, Josefa Oyarzún, Diego Ruiz, Claudio Martínez, Eduardo I Kessi-Pérez, Francisco Salinas
{"title":"A New Set of Optogenetic Switches in Yeast Based on the BcWCL1 Photoreceptor.","authors":"Matías Guerrero, Josefa Oyarzún, Diego Ruiz, Claudio Martínez, Eduardo I Kessi-Pérez, Francisco Salinas","doi":"10.1002/yea.70021","DOIUrl":"https://doi.org/10.1002/yea.70021","url":null,"abstract":"<p><p>Optogenetic switches are molecular systems enabling light-controlled gene expression. These systems are based on the reconstitution of chimeric Transcription Factors (TFs) including a DNA-binding Domain (DBD), a photoreceptor domain, and an Activation Domain (AD). Thus, depending on the light-mediated homodimerization or heteromerization of the chimeric TF, the optogenetic switches can be classified as single-component or two-component systems, respectively. In the budding yeast Saccharomyces cerevisiae, optogenetic switches have shown multiple applications in metabolic engineering and biotechnology. Here, we expand the repertory of optogenetic switches available in yeast, developing a collection of plasmids and yeast strains carrying single-component or two-component optogenetic switches based on the BcWCL1 protein, a blue-light photoreceptor from Botrytis cinerea that contains a LOV (Light Oxygen Voltage) domain. By dissecting the N-terminal, C-terminal, and both protein regions simultaneously, we developed 18 plasmids encoding the BcWCL1 versions fused to the Gal4-DBD and Gal4-AD. Assembled plasmids were combined and transformed into yeast to generate single-component and two-component optogenetic switches, whose blue-light response was measured as transcriptional activity of the luciferase reporter. In general, we observed that the two-component configuration increased the luciferase expression in response to blue-light compared to single-component switches. Importantly, BcWCL1 versions with deletions in the C-terminal region showed the highest luciferase expression upon blue-light stimulation with the lowest background in the dark condition, suggesting that the C-terminal region modulates the blue-light response of this protein. Altogether, we generated new single-component and two-component optogenetic switches, each of them achieving different levels of light-activated luciferase expression, enabling their potential applications in yeast biotechnology.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147783096","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}
Guo-Song Jia, Fang Suo, Ambre Noly, Philippe Fort, Yue Liang, Wen Li, Wen-Cai Zhang, Heng-Le Li, Xiao-Min Du, Fan-Yi Zhang, Tong-Yang Du, Yu Hua, Feng-Yan Bai, Qi-Ming Wang, Michael Brysch-Herzberg, Dominique Helmlinger, Li-Lin Du
{"title":"Schizosaccharomyces Orthogroup (SOG) Resource: A Web Platform for Exploring Gene Conservation in Fission Yeasts.","authors":"Guo-Song Jia, Fang Suo, Ambre Noly, Philippe Fort, Yue Liang, Wen Li, Wen-Cai Zhang, Heng-Le Li, Xiao-Min Du, Fan-Yi Zhang, Tong-Yang Du, Yu Hua, Feng-Yan Bai, Qi-Ming Wang, Michael Brysch-Herzberg, Dominique Helmlinger, Li-Lin Du","doi":"10.1002/yea.70019","DOIUrl":"https://doi.org/10.1002/yea.70019","url":null,"abstract":"<p><p>The fission yeast Schizosaccharomyces pombe is a prominent model organism widely used to investigate fundamental cellular mechanisms. In addition to S. pombe, the genus Schizosaccharomyces includes six other species-S. octosporus, S. japonicus, S. cryophilus, S. osmophilus, S. lindneri, and S. versatilis. These fission yeast species share a common ancestor from which the genus diversified over more than 200 million years. This extensive evolutionary divergence provides opportunities for comparative genomics. Here, we present the Schizosaccharomyces orthogroup (SOG) resource, a web platform developed from our high-quality genome assemblies, gene annotations, and orthology assignments. Most fission yeast genes are assigned to one of over 5,000 orthogroups. The platform enables users to visualize orthogroup sequence alignments and phylogenetic trees, retrieve coding and flanking sequences, and explore the conservation of local synteny. This resource will benefit researchers focusing on individual genes as well as those investigating gene evolution at broader scales. It is freely accessible at https://www.sogweb.org.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147783114","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":"Glucose Restriction Extends Chronological Lifespan of Budding Yeast by Avoiding Commonly Used Auxotrophic Marker Nutrient Starvation.","authors":"Yukinori Ozaki, Taku Ozaki, Qiu-Mei Zhang-Akiyama","doi":"10.1002/yea.70016","DOIUrl":"https://doi.org/10.1002/yea.70016","url":null,"abstract":"<p><p>Dietary restriction (DR) is a robust lifespan-extending intervention across species. While budding yeast is a fundamental model for DR, results from glucose restriction (GR) often show inconsistencies. This may stem from auxotrophic markers in engineered strains, which can induce abnormal cellular states under starvation. We hypothesized that GR extends chronological lifespan (CLS) primarily by avoiding auxotrophic starvation, thereby allowing cells to better adapt to nutrient depletion. Using non-dividing survival assays for precise nutritional control, we observed that yeast survive significantly longer under carbon starvation than under auxotrophic starvation. The extent of CLS extension was diminished when auxotrophic starvation was absent. Yeast cells under auxotrophic starvation showed decreased resistance to H<sub>2</sub>O<sub>2</sub> and increased mutation rate-phenotypes that suggest a failure to enter a robust, quiescent-like state. These findings suggest that auxotrophic starvation may bias not only CLS studies but also broader yeast studies. By reconsidering previous studies with attention to auxotrophic starvation, more meaningful conclusions could emerge. Since auxotrophic nutrients in yeast are analogous to essential amino acids in higher organisms, our findings have broader implications for understanding DR in various species.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147692704","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":"CRISPR/Cas9 Genome Engineering in Non-Conventional Oleaginous Yeasts: Applications, Challenges, and Prospects.","authors":"Rodrigo Gonçalves Dias, Fernanda Pinheiro Moreira Freitas, Eduardo Luís Menezes de Almeida, Luciano Gomes Fietto, Agustin Zsögön, Wendel Batista da Silveira","doi":"10.1002/yea.70015","DOIUrl":"https://doi.org/10.1002/yea.70015","url":null,"abstract":"<p><p>Given the biotechnological potential of yeast-derived oils for oleochemical production, genes encoding lipid metabolism enzymes are key targets for metabolic engineering. Genetic engineering tools such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9, Transcription Activator-Like Effector Nucleases (TALENs), Zinc-Finger Nucleases (ZFNs), RNA interference (RNAi), and integrative plasmids can be used to modulate fatty acid biosynthesis and optimize lipid production. Among them, the CRISPR/Cas9 system, recognized for its simplicity and efficiency, has been deployed as a tool to create oleaginous yeast strains with high lipid productivity and features suitable for application in biorefineries. Species such as Cutaneotrichosporon oleaginosus, Rhodotorula toruloides, Candida spp., and Yarrowia lipolytica have already been engineered using CRISPR/Cas9 to enhance the production of fatty acids and their derivatives. However, designing and constructing an efficient CRISPR/Cas9 platform for oleaginous yeasts faces several hurdles, including low transformation efficiency, difficulties in expressing Cas9 and sgRNAs efficiently and consistently, the lack of well-characterized promoters, limited availability of PAM sequences, and poorly understood DNA repair mechanisms. Here, we address the application of the CRISPR/Cas9 system in oleaginous yeasts, laying out the challenges to developing efficient platforms and highlighting key trends in the field. We compare and discuss alternative CRISPR-Cas9 expression strategies to provide an overview of the current landscape and support the development of new approaches.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":""},"PeriodicalIF":2.6,"publicationDate":"2026-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147487535","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}
YeastPub Date : 2026-01-01Epub Date: 2026-03-04DOI: 10.1002/yea.70011
A Kiely, F O'Halloran, P Young, N F Lowndes, M Grenon, K Finn
{"title":"The Multifaceted Role of Rad9 in the DNA Damage Response of Saccharomyces cerevisiae.","authors":"A Kiely, F O'Halloran, P Young, N F Lowndes, M Grenon, K Finn","doi":"10.1002/yea.70011","DOIUrl":"10.1002/yea.70011","url":null,"abstract":"<p><p>To maintain the integrity of the genome, cells have evolved a complex signalling system, termed the DNA damage response (DDR), which detects DNA damage and promotes DNA repair. To date, over 600 proteins have been identified that play an integral role in the DDR. RAD9, encoding a DDR mediator protein, was the prototypical DNA damage checkpoint gene, establishing the genetic regulation of transient cell-cycle delays upon DNA damage. Rad9, identified 38 years ago in the budding yeast Saccharomyces cerevisiae as a damage-dependent cell-cycle regulator, is now known to regulate additional responses to DNA damage including both cell-cycle recovery and repair. The Rad9 protein is extensively phosphorylated both during a normal cell cycle and following DNA damage and several of these modifications have been linked to specific Rad9 roles within the DDR. Proteins structurally and functionally related to Rad9 exist in mammalian cells (e.g., 53BP1, BRCA1, MDC1) and insights into their regulation and mechanism of action have been informed by studies in yeast. This review will discuss the cellular mechanisms governing the DDR with an emphasis on the multifaceted role of Rad9 in sensing and responding to DNA damage, and how phosphorylation events regulate its function within the DDR. As the cellular events governing the DDR are well conserved, discoveries in yeast can be extrapolated to humans and may lead to the identification of additional novel protein targets, with several DDR inhibitors currently in clinical use or showing promise in clinical trials.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"10-24"},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13067819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147356806","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}
YeastPub Date : 2026-01-01Epub Date: 2026-03-05DOI: 10.1002/yea.70012
Anna Paula O Tironi, Katharina O Barros, Luiz Felipe A Santana, Daniela L Souza, Ana Raquel O Santos, Giovana R Ávila, Thiago M Batista, Glória R Franco, Raphael S Pimenta, Paula B Morais, Marc-André Lachance, Carlos A Rosa, Susana Johann
{"title":"Candidozyma cisalpinoae sp. nov., a Genomically Distinct, Flower-Associated Yeast, Resistant to Azoles and Exhibiting Pathogenicity-Related Traits.","authors":"Anna Paula O Tironi, Katharina O Barros, Luiz Felipe A Santana, Daniela L Souza, Ana Raquel O Santos, Giovana R Ávila, Thiago M Batista, Glória R Franco, Raphael S Pimenta, Paula B Morais, Marc-André Lachance, Carlos A Rosa, Susana Johann","doi":"10.1002/yea.70012","DOIUrl":"10.1002/yea.70012","url":null,"abstract":"<p><p>Six yeast isolates were recovered from Ipomoea flowers collected in the Cerrado biome of Tocantins, Brazil. Sequence analyses of the ITS-5.8S region and the D1/D2 domains of the large subunit (LSU) rRNA gene indicated that these isolates represent a novel species of the genus Candidozyma, phylogenetically related to Candidozyma auris and Ca. ruelliae. A phylogenomic analysis based on 2116 single-copy orthologs from Candidozyma species with available whole-genome sequences showed that the new species, represented by strain UFMG-CM-Y6065, is a sister species to Ca. ruelliae. The name Candidozyma cisalpinoae sp. nov. (MycoBank no. 861366) is proposed to accommodate the new species. The holotype is CBS16108. Sporulation or other evidence of sexual reproduction was not observed, although the genome sequence showed the presence of a functional mating type locus (MATa) and functional pheromone peptides, indicating that the species is haplontic and heterothallic. The species exhibited resistance to multiple antifungals, growth at 42°C, biofilm formation, adhesion to buccal epithelial cells, and expression of efflux pumps, traits of clinical relevance that have been reported for other species in the genus Candidozyma.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"25-37"},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13067812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147366766","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}
YeastPub Date : 2026-01-01Epub Date: 2026-02-19DOI: 10.1002/yea.70010
Isak S Pretorius, Gianni Liti
{"title":"The Three Waters of Yeast Biology: Education, Research and Impact.","authors":"Isak S Pretorius, Gianni Liti","doi":"10.1002/yea.70010","DOIUrl":"10.1002/yea.70010","url":null,"abstract":"","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"5-9"},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146228895","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}
YeastPub Date : 2026-01-01Epub Date: 2026-03-12DOI: 10.1002/yea.70014
Joanna Sękul, Michał Pląder, Katarzyna Rybak, Dorota Derewiaka, Anna Maria Kot, Katarzyna Pobiega
{"title":"Yeasts Isolated From Urban Honeys: Diversity and Potential Application in Mead Production.","authors":"Joanna Sękul, Michał Pląder, Katarzyna Rybak, Dorota Derewiaka, Anna Maria Kot, Katarzyna Pobiega","doi":"10.1002/yea.70014","DOIUrl":"10.1002/yea.70014","url":null,"abstract":"<p><p>This study aimed to isolate, identify, and evaluate yeasts originating from urban honeys as potential starters for mead production. Honey samples from urban apiaries from Poland were analyzed. A total of 47 yeast isolates were obtained and identified as belonging to eight genera: Starmerella, Zygosaccharomyces, Saccharomyces, Rhodotorula, Dothiora, Cystobasidium, Schizosaccharomyces, and Filobasidium. Among them, Starmerella magnoliae was predominant (24 isolates). Zygosaccharomyces rouxii and Z. mellis also occurred frequently. Three Saccharomyces cerevisiae strains (CMIFS 189, CMIFS 191, CMIFS 208) were selected for further trials and applied in the fermentation of trójniak-type meads (honey-to-water ratio 1:2), together with a reference mead starter, Enovini® HONEY (Browin, Poland). Physicochemical analysis showed ethanol contents of 12.22%-15.49%, with CMIFS 191 producing the lowest alcohol but the highest extract. Glycerol levels (0.62%-0.85%) were lower than literature values, while volatile acidity ranged from 0.80 to 1.27 g/L and total acidity from 2.97 to 3.45 g/L. Polyphenol levels (270-299 µg/mL) were high, and antioxidant assays (ABTS, DPPH, RP) showed strain-dependent effects. Volatile analysis revealed alcohols as the dominant group, followed by esters and aldehydes, shaping fruity and floral aroma notes. Based on sensory evaluation, CMIFS 191 showed the highest overall acceptability, whereas the Enovini® HONEY reference starter obtained the lowest sensory scores under the applied conditions. Overall, honey-derived S. cerevisiae strains showed strong potential as novel starters for mead production.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"38-54"},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147436193","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}
YeastPub Date : 2026-01-01Epub Date: 2026-03-14DOI: 10.1002/yea.70013
Laise Cedraz Pinto Matos, Amy Milburn, Chris MacDonald
{"title":"Uptake Mechanisms and Physiological Effects of Furanic Compounds From the Maillard Reaction in Budding Yeast.","authors":"Laise Cedraz Pinto Matos, Amy Milburn, Chris MacDonald","doi":"10.1002/yea.70013","DOIUrl":"10.1002/yea.70013","url":null,"abstract":"<p><p>Maillard reaction products (MRPs) are formed during the thermal processing of foods and exhibit important sensory attributes. Furanic compounds are a subset of MRPs commonly found in food products that are toxic to eukarytoic cells, although the mechanisms of toxicity are poorly understood. We used budding yeast to explore uptake mechanisms of common furanic compounds: 5-hydroxymethylfurfural (HMF), furfural (FUR), and 2-Furyl methyl ketone (FMK). Titrations of each furanic compound were used to identify concentrations that have an inhibitory effect on growth. We identified HMF as a potential substrate of the Pdr5 multidrug resistance pump and linked HMF and FUR toxicity to surface nutrient transporter levels. Live cell imaging shows that HMF disrupts mitochondria whilst FUR affects the endolysosomal system. Results indicate these furanic compounds may have distinct uptake, efflux, and toxicity mechanisms. As many of these cellular components are conserved throughout evolution, this work could shed light on the metabolism of toxic compounds commonly found within animal food sources.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"55-70"},"PeriodicalIF":2.6,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7618920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147460367","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}
YeastPub Date : 2025-12-01Epub Date: 2025-11-24DOI: 10.1002/yea.70008
Jose Ribamar Ferreira-Junior, Vittoria de Lima Camandona, Mario H Barros
{"title":"From Yeast to Therapeutics: Modeling Neurodegenerative Diseases in Saccharomyces cerevisiae.","authors":"Jose Ribamar Ferreira-Junior, Vittoria de Lima Camandona, Mario H Barros","doi":"10.1002/yea.70008","DOIUrl":"10.1002/yea.70008","url":null,"abstract":"<p><p>Here, we review the use of Saccharomyces cerevisiae as a powerful model organism for studying cellular processes implicated in neurodegenerative disorders, including stress responses, proteostasis impairment, and vesicle trafficking defects. Over the last two decades, baker's yeast models have been developed for complex diseases such as Parkinson's, Alzheimer's, Huntington's, and Amyotrophic lateral sclerosis (ALS). Yeast cells expressing human proteins, such as amyloid-β, α-synuclein, huntingtin, and TDP-43, have become crucial tools for high-throughput drug screening aimed at counteracting disease progression. These yeast models have unveiled key components involved in the metabolism and toxicity of these proteins, enabling the identification of interacting partners and novel factors within each pathway. Importantly, these pathways were subsequently shown to be conserved in mammalian models. Furthermore, drug candidates identified using yeast models have provided significant leads for drug discovery, highlighting their potential for developing treatments for these neurodegenerative diseases.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"283-302"},"PeriodicalIF":2.6,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12757828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145588249","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}