FEMS yeast research最新文献_第3页

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 2.4 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":2.4,"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}

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 2.4 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":2.4,"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}

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 2.4 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":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}

引用次数: 0

Aging research has lost a brilliant investigator-Michael Breitenbach, 1943-2024. 衰老研究失去了一位杰出的研究者——迈克尔·布莱滕巴赫（1943 - 2024）。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf008

Ian W Dawes, Terrance G Cooper, Mark Rinnerthaler

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

Advances in CRISPR-enabled genome-wide screens in yeast. 酵母中 CRISPR 驱动的全基因组筛选的进展。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf013

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":"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.","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}

引用次数: 0

The Saccharomyces cerevisiae ∑1278b strain is sensitive to NaCl because of mutations in its ENA1 gene. 酿酒酵母(Saccharomyces cerevisiae)∑1278b菌株对NaCl敏感，其ENA1基因发生突变。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf021

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":"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.","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}

引用次数: 0

Development of a yeast-based sensor platform for evaluation of ligands recognized by the human free fatty acid 2 receptor. 基于酵母的人体游离脂肪酸2受体识别配体传感器平台的开发。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf001

Andrea Clausen Lind, Davi De Castro Gomes, Ricardo Bisquert, Jonas Mårtensson, Martina Sundqvist, Huamei Forsman, Claes Dahlgren, Florian David, Verena Siewers

{"title":"Development of a yeast-based sensor platform for evaluation of ligands recognized by the human free fatty acid 2 receptor.","authors":"Andrea Clausen Lind, Davi De Castro Gomes, Ricardo Bisquert, Jonas Mårtensson, Martina Sundqvist, Huamei Forsman, Claes Dahlgren, Florian David, Verena Siewers","doi":"10.1093/femsyr/foaf001","DOIUrl":"10.1093/femsyr/foaf001","url":null,"abstract":"Yeast-based sensors have shown great applicability for deorphanization of G protein-coupled receptors (GPCRs) and screening of ligands targeting these. A GPCR of great interest is free fatty acid 2 receptor (FFA2R), for which short-chain fatty acids such as propionate and acetate are agonists. FFA2R regulates a wide array of downstream receptor signaling pathways in both adipose tissue and immune cells and has been recognized as a promising therapeutic target, having been implicated in several metabolic and inflammatory diseases. While research aiming to identify ligands recognized by FFA2R for translational applications is ongoing, screening is complicated by the complex regulatory and cell-specific responses mediated by the receptor. To simplify screening towards identification of novel ligands, heterologous platforms are valuable tools that offer efficient identification of ligand activity in the absence of regulatory mechanisms. Here, we present a yeast-based sensor designed to evaluate G protein α i1-mediated FFA2R signaling, with an assay time of 3 h. We verify this platform towards the natural agonists, propionate and acetate, and show applicability towards evaluation of synthetic agonists, antagonists, and allosteric agonists. As such, we believe that the developed yeast strain constitutes a promising screening platform for effective evaluation of ligands acting on FFA2R.","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/PMC11781196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002734","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

Image-based quantification of Candida albicans filamentation and hyphal length using the open-source visual programming language JIPipe. 使用开源可视化编程语言JIPipe对白色念珠菌丝状和菌丝长度进行图像量化。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf011

Jan-Philipp Praetorius, Sophia U J Hitzler, Mark S Gresnigt, Marc Thilo Figge

{"title":"Image-based quantification of Candida albicans filamentation and hyphal length using the open-source visual programming language JIPipe.","authors":"Jan-Philipp Praetorius, Sophia U J Hitzler, Mark S Gresnigt, Marc Thilo Figge","doi":"10.1093/femsyr/foaf011","DOIUrl":"10.1093/femsyr/foaf011","url":null,"abstract":"The formation of hyphae is one of the most crucial virulence traits the human pathogenic fungus Candida albicans possesses. The assessment of hyphal length in response to various stimuli, such as exposure to human serum, provides valuable insights into the adaptation strategies of C. albicans to the host environment. Despite the increasing high-throughput capacity live-cell imaging and data generation, the accurate analysis of hyphal growth has remained a laborious, error-prone, and subjective manual process. We developed an analysis pipeline utilizing the open-source visual programming language Java Image Processing Pipeline (JIPipe) to overcome the limitations associated with manual analysis of hyphal growth. By comparing our automated approach with manual analysis, we refined the strategies to achieve accurate differentiation between yeast cells and hyphae. The automated method enables length measurements of individual hyphae, facilitating a time-efficient, high-throughput, and user-friendly analysis. By utilizing this JIPipe analysis approach, we obtained insights into the filamentation behavior of two C. albicans strains when exposed to human serum albumin (HSA), the most abundant protein in human serum. Our findings indicate that despite the known role of HSA in stimulating fungal growth, it reduces filamentous growth. The implementation of our automated JIPipe analysis approach for hyphal growth represents a long-awaited and time-efficient solution to meet the demand of high-throughput data generation. This tool can benefit different research areas investigating the virulence aspects of C. albicans.","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/PMC11963753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623946","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

Metabolic engineering of yeast to efficiently synthesize heme and hemoproteins: recent advance and prospects. 酵母高效合成血红素和血红蛋白的代谢工程研究进展与展望。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf019

Haibo Yu, Yunpeng Wang, Yijie Wang, Yueheng Niu, Jingwen Zhou, Jianghua Li, Jian Chen, Guocheng Du, Xinrui Zhao

引用次数: 0