IF 2.2 4区生物学

Yeast Pub Date : 2026-07-01 Epub Date: 2026-05-14 DOI: 10.1002/yea.70024

Devanshu V Mehta, Mary T Serviss, Keith R Schneider, Renee Goodrich, Andrew J MacIntosh

{"title":"The Role of Mannose in Saccharomyces pastorianus Flocculation During Industrial Brewing Fermentations.","authors":"Devanshu V Mehta, Mary T Serviss, Keith R Schneider, Renee Goodrich, Andrew J MacIntosh","doi":"10.1002/yea.70024","DOIUrl":"10.1002/yea.70024","url":null,"abstract":"Yeast flocculation is a phenomenon in which yeast zymolectins bind to mannose on adjacent cells resulting in aggregation within fermentation media. Flocculation has been extensively studied and is often assumed to occur only after media sugars are depleted as these are thought to competitively bind to zymolectins. However, yeast within the brewing industry have often been observed flocculating prematurely or staying suspended after media sugars were depleted. In this study, the mechanism of yeast (Saccharomyces pastorianus) flocculation was further investigated, specifically, how flocculation ability, zymolectins, and mannose associated with yeast cells changed throughout fermentation. It was observed that yeast flocculation behavior changed throughout fermentation despite no changes in zymolectin concentrations (as measured using bound fluoroprobes) independent of media sugar concentration. However, a strong positive correlation was observed between yeast flocculation ability and mannose concentration which increased as the fermentation progressed. This implies that the changes observed in flocculation behavior during fermentation may be more dependent on cell mannose rather than media sugars or lectins. These results have implications for yeast immobilization and flocculation control schemes. This research enhances the current understanding of the yeast flocculation mechanism with applications in brewing, bioethanol production, pharmaceutical production, precision fermentation, and cell biomass industries.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"159-169"},"PeriodicalIF":2.2,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147933977","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}

引用次数: 0

rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences. rnamine：长重复序列分析的新工具。

IF 2.2 4区生物学

Yeast Pub Date : 2026-07-01 Epub Date: 2026-05-26 DOI: 10.1002/yea.70023

Agnieszka Czarnocka-Cieciura, Natalia Gumińska

{"title":"rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.","authors":"Agnieszka Czarnocka-Cieciura, Natalia Gumińska","doi":"10.1002/yea.70023","DOIUrl":"10.1002/yea.70023","url":null,"abstract":"In this study, we introduce a novel approach for analysing long, repetitive genomic sequences. Our methods significantly advance research on rDNA polymorphism. First, we describe a technique for isolating high-molecular-weight DNA from individual chromosomes, enabling selective enrichment of sequencing libraries for extensive genomic regions of interest. Second, we present rDNAmine, a bioinformatic toolkit for capturing and examining large repetitive arrays in Oxford Nanopore sequencing data. This approach facilitates the study of polymorphisms within long repeats, bypassing traditional alignment-based methods and providing a more efficient and scalable solution for investigating repetitive regions. We demonstrate the effectiveness of our approach through the analysis of rDNA arrays in two yeast species, Saccharomyces cerevisiae and Candida albicans. In S. cerevisiae, rDNA arrays show limited polymorphism, while in C. albicans, we observe substantial variation in rDNA module size, with two distinct repeat populations within the array. These findings reveal species-specific differences in the structural organisation of rDNA loci, highlighting the diverse nature of tandem repeat architecture. The rDNAmine toolkit is broadly applicable to various organisms and repetitive genomic contexts, offering a versatile platform for studying repetitive sequences.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"170-183"},"PeriodicalIF":2.2,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13340991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148035938","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

Comparative Analysis of Stress Adaptation in the Yeast Microbiome of Cactus. 仙人掌酵母菌群的逆境适应比较分析。

IF 2.2 4区生物学

Yeast Pub Date : 2026-06-23 DOI: 10.1002/yea.70033

Alya N Hussain, Kevin T Fotso, Michael A McMurray

引用次数: 0

CRISPR/Cas9 Genome Engineering in Non-Conventional Oleaginous Yeasts: Applications, Challenges, and Prospects. CRISPR/Cas9基因组工程在非常规产油酵母中的应用、挑战和前景

IF 2.2 4区生物学

Yeast Pub Date : 2026-05-01 Epub Date: 2026-03-19 DOI: 10.1002/yea.70015

Rodrigo Gonçalves Dias, Fernanda Pinheiro Moreira Freitas, Eduardo Luís Menezes de Almeida, Luciano Gomes Fietto, Agustin Zsögön, Wendel Batista da Silveira

{"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":"10.1002/yea.70015","url":null,"abstract":"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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"77-88"},"PeriodicalIF":2.2,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13159405/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Schizosaccharomyces Orthogroup (SOG) Resource: A Web Platform for Exploring Gene Conservation in Fission Yeasts. Schizosaccharomyces Orthogroup （SOG）资源：一个探索裂变酵母基因保护的网络平台。

IF 2.2 4区生物学

Yeast Pub Date : 2026-05-01 Epub Date: 2026-04-22 DOI: 10.1002/yea.70019

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":"10.1002/yea.70019","url":null,"abstract":"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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"101-111"},"PeriodicalIF":2.2,"publicationDate":"2026-05-01","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}

引用次数: 0

A New Set of Optogenetic Switches in Yeast Based on the BcWCL1 Photoreceptor. 一组基于BcWCL1光感受器的酵母光遗传开关。

IF 2.2 4区生物学

Yeast Pub Date : 2026-05-01 Epub Date: 2026-04-29 DOI: 10.1002/yea.70021

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":"10.1002/yea.70021","url":null,"abstract":"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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"112-123"},"PeriodicalIF":2.2,"publicationDate":"2026-05-01","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}

引用次数: 0

Glucose Restriction Extends Chronological Lifespan of Budding Yeast by Avoiding Commonly Used Auxotrophic Marker Nutrient Starvation. 葡萄糖限制通过避免常用的营养不良标记物营养饥饿延长出芽酵母的时间顺序寿命。

IF 2.2 4区生物学

Yeast Pub Date : 2026-05-01 Epub Date: 2026-04-15 DOI: 10.1002/yea.70016

Yukinori Ozaki, Taku Ozaki, Qiu-Mei Zhang-Akiyama

{"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":"10.1002/yea.70016","url":null,"abstract":"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 H2O2 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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"89-100"},"PeriodicalIF":2.2,"publicationDate":"2026-05-01","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}

引用次数: 0

The Multifaceted Role of Rad9 in the DNA Damage Response of Saccharomyces cerevisiae. Rad9在酿酒酵母DNA损伤反应中的多重作用。

IF 2.2 4区生物学

Yeast Pub Date : 2026-01-01 Epub Date: 2026-03-04 DOI: 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":"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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"10-24"},"PeriodicalIF":2.2,"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}

引用次数: 0

Candidozyma cisalpinoae sp. nov., a Genomically Distinct, Flower-Associated Yeast, Resistant to Azoles and Exhibiting Pathogenicity-Related Traits. 假丝酵母菌cisalpinoae sp. nov.，一种基因组上独特的花相关酵母菌，对氮唑具有抗性，并表现出与致病性相关的性状。

IF 2.2 4区生物学

Yeast Pub Date : 2026-01-01 Epub Date: 2026-03-05 DOI: 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":"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.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"25-37"},"PeriodicalIF":2.2,"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}

引用次数: 0

The Three Waters of Yeast Biology: Education, Research and Impact. 酵母生物学的三个领域：教育、研究和影响。

IF 2.6 4区生物学

Yeast Pub Date : 2026-01-01 Epub Date: 2026-02-19 DOI: 10.1002/yea.70010

Isak S Pretorius, Gianni Liti

引用次数: 0

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