FEMS yeast research最新文献_第9页

Evolutionary engineering and molecular characterization of an antimycin A-resistant Saccharomyces cerevisiae strain: the key role of pleiotropic drug resistance (PDR1). 一株抗霉素a耐药酿酒酵母的进化工程和分子特征：多效耐药的关键作用。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf062

Alican Topaloğlu, Can Holyavkin, Ömer Esen, Ogün Morkoç, Karl Persson, Cecilia Geijer, Zeynep Petek Çakar

{"title":"Evolutionary engineering and molecular characterization of an antimycin A-resistant Saccharomyces cerevisiae strain: the key role of pleiotropic drug resistance (PDR1).","authors":"Alican Topaloğlu, Can Holyavkin, Ömer Esen, Ogün Morkoç, Karl Persson, Cecilia Geijer, Zeynep Petek Çakar","doi":"10.1093/femsyr/foaf062","DOIUrl":"10.1093/femsyr/foaf062","url":null,"abstract":"Antimycin A, an antifungal agent that inhibits mitochondrial respiration, provides a useful model for studying resistance mechanisms. Antifungal resistance is an escalating clinical concern with limited treatment options available. To understand the molecular mechanisms of antimycin A resistance, a genetically stable, antimycin A-resistant Saccharomyces cerevisiae strain was successfully developed for the first time through an evolutionary engineering strategy, based on long-term systematic application of gradually increasing antimycin A stress in repetitive batch cultures without prior chemical mutagenesis. Comparative whole genome resequencing analysis of the evolved strain ant905-9 revealed two missense mutations in PDR1 and PRP8 genes involved in pleiotropic drug resistance and RNA splicing, respectively. Using CRISPR/Cas9 genome editing tools, the identified mutations were introduced individually and together into the reference strain, and it was confirmed that the Pdr1p.M732R mutation alone confers antimycin A-resistance in S. cerevisiae. Comparative transcriptomic analysis of the reverse-engineered Pdr1p.M732R strain showed alterations in PDR (pleiotropic drug resistance), transmembrane transport, vesicular trafficking, and autophagy pathways. Our results highlight the potential key role of PDR1 in antifungal drug resistance. This study provides new insights into mitochondrial drug resistance and the adaptive potential of yeast under respiratory stress.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12570882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145307391","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

Engineering recombination machinery facilitates the construction of yeast cell factories. 工程重组机械有利于酵母细胞工厂的建设。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf066

Nan Jia, Yongjin J Zhou, Jiaoqi Gao

引用次数: 0

Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices. 不同来源的康普茶微生物群落和发酵方法的综合调查。

IF 2.7 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf005

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":"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.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.7,"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}

引用次数: 0

Functional analysis of Candida albicans Cdr1 through homologous and heterologous expression studies. 通过同源和异源表达研究分析白色念珠菌 Cdr1 的功能。

IF 2.7 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf012

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":"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.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.7,"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}

引用次数: 0

Cdr1 in focus: a personal reflection on multidrug transporter research. 聚焦Cdr1：对多药转运体研究的个人反思。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf003

Rajendra Prasad

{"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":"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.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"25 ","pages":""},"PeriodicalIF":3.5,"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}

引用次数: 0

Lipid-dependent growth of Malassezia spp. in defined medium with single fatty acids. 马拉色菌在含单一脂肪酸的培养基中的脂质依赖性生长。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf043

Janny Liebregts, Lars van der Velden, Angie Lorena Fonseca-Fernández, Adriana Marcela Celis Ramírez, Hans de Cock

{"title":"Lipid-dependent growth of Malassezia spp. in defined medium with single fatty acids.","authors":"Janny Liebregts, Lars van der Velden, Angie Lorena Fonseca-Fernández, Adriana Marcela Celis Ramírez, Hans de Cock","doi":"10.1093/femsyr/foaf043","DOIUrl":"10.1093/femsyr/foaf043","url":null,"abstract":"Details on fatty acid and lipid metabolism in Malassezia spp. are limited, amongst others, because efficient growth of Malassezia spp. in defined media with free fatty acids has not yet been described. Here, we describe a culturing method in a defined medium in which lipid-dependent growth of Malassezia spp. can be studied. We observed efficient growth of Malassezia furfur and Malassezia pachydermatis in liquid minimal medium supplemented with palmitic acid in the presence of NP-40 Tergitol™. We introduced a 3-day fatty acid-starvation phase to reduce residual growth due to the carry-over of lipids from rich media. The Malassezia spp. studied remained viable longer in liquid media lacking fatty acids and detergents, as described previously for a Saccharomyces cerevisiae fas1 mutant. This suggests that Malassezia spp. might have developed mechanisms to survive periods of fatty acid starvation. We compared the lipidome of both Malassezia species grown in mDixon or a defined medium with NP-40 Tergitol™ supplemented with either palmitate and/or oleic acid, or ox bile. Remarkably, the lipidome of mDixon grown cells is enriched in lipid species associated with lipid droplets. Malassezia spp. adapt their lipid composition after growth in a defined medium, and a subset of novel lipid species was identified.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12416284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144948292","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

Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi as a potential host for biorefinery. 揭示嗜酸酵母buldermaudiozyma作为生物炼制潜在宿主的低pH响应的遗传基础。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf053

Laura Natalia Balarezo-Cisneros, Alistair Hanak, Leo Zeef, Aleksandr Mironov, Fernando Valle, Daniela Delneri

{"title":"Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi as a potential host for biorefinery.","authors":"Laura Natalia Balarezo-Cisneros, Alistair Hanak, Leo Zeef, Aleksandr Mironov, Fernando Valle, Daniela Delneri","doi":"10.1093/femsyr/foaf053","DOIUrl":"10.1093/femsyr/foaf053","url":null,"abstract":"Nonconventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of nonconventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the expressional and morphological changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi and Saccharomyces bulderi): CBS 8638, CBS 8639, and NRRL Y-27205. The comparison of the transcriptome of cells growing in a bioreactor at pH = 5.5 vs pH = 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL Y-27205 the least acidophilic strain, showing the largest transcriptional response when compared to the other strains. We identified four uncharacterized genes, unique to M. bulderi, and predicted function as transporters, upregulated at low pH. Microscopy studies showed that M. bulderi cell wall is not damaged in acidic environment, and the membrane lipid composition remains stable at low pH, unlike Saccharomyces cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12509841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091616","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

Evolution and applications of genome-scale metabolic models in yeast systems biology studies. 基因组尺度代谢模型在酵母系统生物学研究中的进化与应用

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf045

Xiaodan He, Hongzhong Lu

引用次数: 0

Yeast as a tool for exploring disulfide-rich peptides. 酵母作为探索富含二硫化物肽的工具。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf069

Kuok Yap, Owen T Porth, Jing Xie, Conan K Wang, Thomas Durek, K Dane Wittrup, David J Craik

{"title":"Yeast as a tool for exploring disulfide-rich peptides.","authors":"Kuok Yap, Owen T Porth, Jing Xie, Conan K Wang, Thomas Durek, K Dane Wittrup, David J Craik","doi":"10.1093/femsyr/foaf069","DOIUrl":"10.1093/femsyr/foaf069","url":null,"abstract":"Cyclic disulfide-rich peptides have become increasingly popular in drug development because their structures enhance molecular stability and allow for mutagenesis to introduce non-native functions. This review focuses on yeast-based platform technologies and their utility in advancing cyclic disulfide-rich peptides as drug modalities and for large-scale biomanufacturing. These technologies include yeast surface display which facilitates the screening of large libraries to develop peptide binders with strong affinity and selectivity for protein targets, while maintaining the innate high stability of the peptide scaffold via protease-based selection pressure. We also describe a recently developed platform that leverages yeast's ability to secrete correctly folded disulfide-rich peptides while simultaneously displaying peptide or protein tags on their surfaces. In combination with microfluidics technology, the platform creates single-cell yeast-in-droplets reactors, enabling the screening of large libraries based on functional output rather than solely on binding affinity. After identifying cyclic peptide candidates through library-based discovery, these candidates can be produced using a versatile yeast-based bioproduction platform. Traditionally, cyclic disulfide-rich peptides are produced through solid-phase synthesis, a method that generates significant amounts of toxic waste. In contrast, yeast-based bioproduction offers an environmentally sustainable alternative. It has the capability to produce structurally distinct peptides with minimal adjustments and is easily scalable using microbial fermenters, making it an ideal choice for large-scale production.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12715861/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774057","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

Improving cellulosic ethanol production by an engineered yeast consortium displaying a pentafunctional mini-cellulosome. 展示五功能微型纤维素体的工程酵母改善纤维素乙醇生产。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf022

Xiaofei Song, Jianze Zhang, Siyu Fu, Ziyi Liu, Yan Chen, Tingheng Zhu

{"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":"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%.","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}

引用次数: 0