{"title":"Exploring pectinolytic yeast diversity: toward effective polygalacturonase producers for applications in wine-making.","authors":"Mehmet Gazaloğlu, Carole Camarasa, Elke Nevoigt","doi":"10.1093/femsyr/foae033","DOIUrl":"10.1093/femsyr/foae033","url":null,"abstract":"<p><p>Pectinolytic enzymes secreted by yeasts have an untapped potential in industry, particularly in wine-making. This study addresses the limitations of the current screening methods in reliably predicting the capacity of pectinolytic yeast strains to secrete polygalacturonase (PGase) under industrial conditions, suggesting a novel screening approach. Using the context of wine-making as an example, a diverse collection of 512 yeast strains from 17 species was analysed for PGase secretion, a key enzyme in pectinolysis. The traditional halo assay on solid yeast-pepton-dextrose (YPD) medium revealed 118 strains from nine genera being PGase positive. Screening these strains by incubating them at 20°C on a solid synthetic grape juice medium containing polygalacturonic acid (PG) significantly reduced the number of promising strains to 35. They belong to five genera: Kluyveromyces sp., Cryptococcus, Pichia, Torulaspora, and Rhodotorula. Afterward, a newly developed pectin-iodine assay was used to precisely quantify the PGase activity of the best-performing strains in a liquid medium. Strains from Kluyveromyces and Cryptococcus sp. stood out regarding high pectinolytic activity. Our methodological advancements tailored to identify highly promising pectinolytic yeasts for industrial use open new avenues for wine-making and other industrial processes encompassing media rich in pectin and sugars.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781195/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142852962","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}
Guangchun Lu, Li Liu, Mitchell Opoku, Ruifan Zhu, Haiyang Wang, Gang Feng
{"title":"Characterization of oncohistone H2B variants in Schizosaccharomyces pombe reveals a key role of H2B monoubiquitination deficiency in genomic instability by altering gene expression.","authors":"Guangchun Lu, Li Liu, Mitchell Opoku, Ruifan Zhu, Haiyang Wang, Gang Feng","doi":"10.1093/femsyr/foaf027","DOIUrl":"10.1093/femsyr/foaf027","url":null,"abstract":"<p><p>Various amino acid substitutions commonly occur at one residue of a histone in human cancers, but it remains unclear whether these histone variants have distinct oncogenic effects and mechanisms. Our previous modeling study in the fission yeast Schizosaccharomyces pombe demonstrated that the oncohistone mutants H2BG52D, H2BD67N, and H2BP102L cause the homologous recombination defects and genomic instability by compromising H2B monoubiquitination (H2Bub). However, it is unknown whether other amino acid changes at the H2B-Gly52/Asp67/Pro102 residues influence H2Bub levels and whether they cause genomic instability by altering H2Bub-regulated gene expression. Here, we construct diverse oncomutants at the sole H2B gene htb1-Gly52/Asp67/Pro102 sites in S. pombe and study their impacts on genotoxic response, H2Bub levels, and gene expression. Interestingly, the oncomutants htb1-G52D, htb1-D67N, and htb1-P102L exclusively exhibit significant genotoxic sensitivity, reduced H2Bub levels, and altered gene expression. These defects can be rescued by restoring H2Bub levels with the deletion of the H2B deubiquitinase ubp8+. These strong genetic correlations suggest that H2Bub deficiency plays a determinant role in the genomic instability of htb1-Gly52/Asp67/Pro102 oncomutants and that the alteration of gene expression due to reduced H2Bub levels is a novel mechanism underlying the genomic instability caused by htb1-G52D, htb1-D67N, and htb1-P102L oncomutations.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12128920/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144127063","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}
Mengcun Zhao, Erwin Lamping, Kyoko Niimi, Masakazu Niimi, Richard D Cannon
{"title":"Functional analysis of Candida albicans Cdr1 through homologous and heterologous expression studies.","authors":"Mengcun Zhao, Erwin Lamping, Kyoko Niimi, Masakazu Niimi, Richard D Cannon","doi":"10.1093/femsyr/foaf012","DOIUrl":"10.1093/femsyr/foaf012","url":null,"abstract":"<p><p>Candida albicans Cdr1 is a plasma membrane ATP-binding cassette transporter encoded by CDR1 that was first cloned 30 years ago in Saccharomyces cerevisiae. Increased expression of Cdr1 in C. albicans clinical isolates results in resistance to azole antifungals due to drug efflux from the cells. Knowledge of Cdr1 structure and function could enable the design of Cdr1 inhibitors that overcome efflux-mediated drug resistance. This article reviews the use of expression systems to study Cdr1. Since the discovery of CDR1 in 1995, 123 studies have investigated Cdr1 using either heterologous or homologous expression systems. The majority of studies have employed integrative transformation and expression in S. cerevisiae. We describe a suite of plasmids with a range of useful protein tags for integrative transformation that enable the creation of tandem-gene arrays stably integrated into the S. cerevisiae genome, and a model for Cdr1 transport function. While expression in S. cerevisiae generates a strong phenotype and high yields of Cdr1, it is a nonnative environment and may result in altered structure and function. Membrane lipid composition and architecture affects membrane protein function and a focus on homologous expression in C. albicans may permit a more accurate understanding of Cdr1 structure and function.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974388/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143656597","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":"Cdr1 in focus: a personal reflection on multidrug transporter research.","authors":"Rajendra Prasad","doi":"10.1093/femsyr/foaf003","DOIUrl":"10.1093/femsyr/foaf003","url":null,"abstract":"<p><p>Drug resistance mechanisms in human pathogenic Candida species are constantly evolving. Over time, these species have developed diverse strategies to counter the effects of various drug classes, making them a significant threat to human health. In addition to well-known mechanisms such as drug target modification, overexpression, and chromosome duplication, Candida species have also developed permeability barriers to antifungal drugs through reduced drug import or increased efflux. The genomes of Candida species contain a multitude of drug resistance genes, many of which encode membrane efflux transporters that actively expel drugs, preventing their toxic accumulation inside the cells and contributing to multidrug resistance. This brief personal retrospective piece for the \"Thematic Issue on Celebrating 30 Years of Cdr1 Research: new trends in antifungal therapy and drug resistance\" looks back as to how antifungal research has shifted focus since the identification of the first multidrug transporter gene, CDR1 (Candida Drug Resistance 1), leading to new insights into how reduced azole permeability across Candida cell membranes influences antifungal susceptibility.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"25 ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064866","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}
Emna Ben Saad, Anne Friedrich, Frédérique Fischer, Olivier Courot, Joseph Schacherer, Claudine Bleykasten
{"title":"Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices.","authors":"Emna Ben Saad, Anne Friedrich, Frédérique Fischer, Olivier Courot, Joseph Schacherer, Claudine Bleykasten","doi":"10.1093/femsyr/foaf005","DOIUrl":"10.1093/femsyr/foaf005","url":null,"abstract":"<p><p>Kombucha is a unique, naturally fermented sweetened tea produced for thousands of years, relying on a symbiotic microbiota in a floating biofilm, used for successive fermentations. The microbial communities consist of yeast and bacteria species, distributed across two phases: the liquid and the biofilm fractions. In the fermentation of kombucha, various starters of different shapes and origins are used, and there are multiple brewing practices. By metabarcoding, we explored here the consortia and their evolution from a collection of 23 starters coming from various origins summarizing the diversity of kombucha fermentation processes. A core microbiota of yeast and bacteria has been identified in these diverse kombucha symbiotic consortia, revealing consistent core taxa across symbiotic consortium of bacteria and yeasts from different starters. The common core consists of five taxa: two yeast species from the Brettanomyces genus (B. bruxellensis and B. anomalus) and bacterial taxa Komagataeibacter, Lactobacillus, and Acetobacteraceae, including the Acetobacter genus. The distribution of yeast and bacteria core taxa differs between the liquid and biofilm fractions, as well as between the \"mother\" and \"daughter\" biofilms used in successive fermentations. In terms of microbial composition, the diversity is relatively low, with only a few accessory taxa identified. Overall, our study provides a deeper understanding of the core and accessory taxa involved in kombucha fermentation.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188642","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":"Aging research has lost a brilliant investigator-Michael Breitenbach, 1943-2024.","authors":"Ian W Dawes, Terrance G Cooper, Mark Rinnerthaler","doi":"10.1093/femsyr/foaf008","DOIUrl":"10.1093/femsyr/foaf008","url":null,"abstract":"","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929133/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143575599","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":"Improving cellulosic ethanol production by an engineered yeast consortium displaying a pentafunctional mini-cellulosome.","authors":"Xiaofei Song, Jianze Zhang, Siyu Fu, Ziyi Liu, Yan Chen, Tingheng Zhu","doi":"10.1093/femsyr/foaf022","DOIUrl":"10.1093/femsyr/foaf022","url":null,"abstract":"<p><p>As a traditional ethanol-producing microorganism, Saccharomyces cerevisiae is an ideal host for consolidated bioprocessing. However, when overloaded cellulase genes are expressed in yeast, the metabolic burden on cells may greatly affect cell growth and cellulosic ethanol production. In this study, we developed a yeast consortium system that secretes and assembles five types of cellulases on the yeast cell surface to improve cellulosic ethanol production. This system involves one display strain, which provides the scaffoldin on the surface and several secretion strains that secrete each cellulase. The secreted dockerin-containing enzymes, cellobiohydrolase (CBH), endoglucanase (EG), β-glucosidase (BGL), cellobiose dehydrogenase (CDH), and lytic polysaccharide monooxygenase (LPMO), were randomly assembled to the scaffoldin to generate a pentafunctional mini-cellulosome via cohesion-dockerin interactions. The developed system relieved the metabolic burden placed on the engineered single yeast strain and leveraged the innate metabolic potential of each host. In addition, the enzymes in the consortium acted synergistically and efficiently boosted cellulose degradation and ethanol production. When compared with the conventional system, this consortium system increased the ethanol titers from 2.66 to 4.11 g/l with phosphoric acid swollen cellulose (PASC) as the substrate, an improvement of 55%. With Avicel as the substrate, ethanol titers increased from 1.57 to 3.24 g/l, representing an enhancement of 106%.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12108760/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144110440","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}
David Engelberg, Alexey Baskin, Shelly Ben Zaken, Irit Marbach
{"title":"The Saccharomyces cerevisiae ∑1278b strain is sensitive to NaCl because of mutations in its ENA1 gene.","authors":"David Engelberg, Alexey Baskin, Shelly Ben Zaken, Irit Marbach","doi":"10.1093/femsyr/foaf021","DOIUrl":"10.1093/femsyr/foaf021","url":null,"abstract":"<p><p>Most laboratory strains of the yeast Saccharomyces cerevisiae are incapable of invading agar, to form large colonies (mats), and to develop filament-like structures (pseudohyphae). A prominent strain that manifests these morphologies is ∑1278b. While induced transcription of the FLO11 gene is critical for executing invasive growth, mat formation, and pseudohyphal growth, downregulation of the 'general stress response' also seems to be required. As this response is weak in ∑1278b cells, we assumed that they may be sensitives to stresses. We report, however, that they are resistant to various stressors, but severely sensitive specifically to NaCl. We found that this sensitivity is a result of mutations in the single ∑1278b's ENA gene, encoding P-type sodium ATPase. Other laboratory strains harbor three to five copies of ENA, suggesting that ∑1278b was selected against Ena activity. Obtaining ∑1278b cells that can grow on NaCl allows checking its effect on colony morphologies. In the presence of NaCl, ∑1278b/ENA1+ cells do not invade agar, and do not form pseudohyphae or mats. Thus, we have found the following: (i) The ∑1278b strain differs from other laboratory strains with respect to sensitivity to NaCl, because it has no active Na+ ATPase exporter. (ii) NaCl is a suppressor of invasiveness, filamentous growth, and mat formation.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12091097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960109","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}
Nicholas R Robertson, Sangcheon Lee, Aida Tafrishi, Ian Wheeldon
{"title":"Advances in CRISPR-enabled genome-wide screens in yeast.","authors":"Nicholas R Robertson, Sangcheon Lee, Aida Tafrishi, Ian Wheeldon","doi":"10.1093/femsyr/foaf013","DOIUrl":"10.1093/femsyr/foaf013","url":null,"abstract":"<p><p>Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas genome-wide screens are powerful tools for unraveling genotype-phenotype relationships, enabling precise manipulation of genes to study and engineer industrially useful traits. Traditional genetic methods, such as random mutagenesis or RNA interference, often lack the specificity and scalability required for large-scale functional genomic screens. CRISPR systems overcome these limitations by offering precision gene targeting and manipulation, allowing for high-throughput investigations into gene function and interactions. Recent work has shown that CRISPR genome editing is widely adaptable to several yeast species, many of which have natural traits suited for industrial biotechnology. In this review, we discuss recent advances in yeast functional genomics, emphasizing advancements made with CRISPR tools. We discuss how the development and optimization of CRISPR genome-wide screens have enabled a host-first approach to metabolic engineering, which takes advantage of the natural traits of nonconventional yeast-fast growth rates, high stress tolerance, and novel metabolism-to create new production hosts. Lastly, we discuss future directions, including automation and biosensor-driven screens, to enhance high-throughput CRISPR-enabled yeast engineering.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11995697/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143669128","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":"Assessing methods for estimating microbial lag phase duration: a comparative analysis using Saccharomyces cerevisiae empirical and simulated data.","authors":"Monika Opalek, Dominika Wloch-Salamon, Bogna J Smug","doi":"10.1093/femsyr/foaf033","DOIUrl":"10.1093/femsyr/foaf033","url":null,"abstract":"<p><p>The lag phase is a temporary, nonreplicative period observed when a microbial population is introduced to a new, nutrient-rich environment. Although the theoretical concept of growth phases is clear, the practical application of methods for estimating lag lengths is often challenging. In fact, there are two distinct assumptions: (i) that cells do not divide at all during the lag phase or (ii) that they divide but at a suboptimal rate. Therefore, the choice of method should consider not only technical limitations but also consistency with the biological context. Here, we investigate the performance of the most common lag estimation methods, using empirical and simulated datasets. We apply different biological scenarios and simulate curves with varying parameters (i.e. growth rate, noise level, and frequency of measurements) to test their impact on the estimated lag phase duration. Our validation shows that infrequent measurements, low growth rate, longer lag phases, or higher level of noise in the measurements result in higher bias and higher variance of lag estimation. Additionally, in case of noisy data, the methods relying on model fitting perform best.</p>","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12258147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607893","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}