FEMS yeast research最新文献_第2页

Advancing recombinant protein expression in Komagataella phaffii: opportunities and challenges.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf010

Wen Lv, Menghao Cai

{"title":"Advancing recombinant protein expression in Komagataella phaffii: opportunities and challenges.","authors":"Wen Lv, Menghao Cai","doi":"10.1093/femsyr/foaf010","DOIUrl":"10.1093/femsyr/foaf010","url":null,"abstract":"Komagataella phaffii has gained recognition as a versatile platform for recombinant protein production, with applications covering biopharmaceuticals, industrial enzymes, food additives, etc. Its advantages include high-level protein expression, moderate post-translational modifications, high-density cultivation, and cost-effective methanol utilization. Nevertheless, it still faces challenges for the improvement of production efficiency and extension of applicability. This review highlights the key strategies used to facilitate productivity in K. phaffii, including systematic advances in genetic manipulation tools, transcriptional and translational regulation, protein folding and secretion optimization. Glycosylation engineering is also concerned as it enables humanized glycosylation profiles for the use in therapeutic proteins and functional food additivities. Omics technologies and genome-scale metabolic models provide new insights into cellular metabolism, enhancing recombinant protein expression. High-throughput screening technologies are also emphasized as crucial for constructing high-expression strains and accelerating strain optimization. With advancements in gene-editing, synthetic and systems biology tools, the K. phaffii expression platform has been significantly improved for fundamental research and industrial use. Future innovations aim to fully harness K. phaffii as a next-generation cell factory, providing efficient, scalable, and cost-effective solutions for diverse applications. It continues to hold promise as a key driver in the field of biotechnology.","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/PMC11934926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143614074","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

Insights into the genomic and phenotypic diversity of Monosporozyma unispora strains isolated from anthropic environments.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf016

Frédéric Bigey, Xavière Menatong Tene, Marc Wessner, Hugo Devillers, Martine Pradal, Corinne Cruaud, Jean-Marc Aury, Cécile Neuvéglise

{"title":"Insights into the genomic and phenotypic diversity of Monosporozyma unispora strains isolated from anthropic environments.","authors":"Frédéric Bigey, Xavière Menatong Tene, Marc Wessner, Hugo Devillers, Martine Pradal, Corinne Cruaud, Jean-Marc Aury, Cécile Neuvéglise","doi":"10.1093/femsyr/foaf016","DOIUrl":"10.1093/femsyr/foaf016","url":null,"abstract":"Food microorganisms have been employed for centuries for the processing of fermented foods, leading to adapted populations with phenotypic traits of interest. The yeast Monosporozyma unispora (formerly Kazachstania unispora) has been identified in a wide range of fermented foods and beverages. Here, we studied the genetic and phenotypic diversity of a collection of 53 strains primarily derived from cheese, kefir, and sourdough. The 12.7-Mb genome of the type strain CLIB 234T was sequenced and assembled into near-complete chromosomes and annotated at the structural and functional levels, with 5639 coding sequences predicted. Comparison of the pangenome and core genome revealed minimal differences. From the complete yeast collection, we gathered genetic data (diversity, phylogeny, and population structure) and phenotypic data (growth capacity on solid media). Population genomic analyses revealed a low level of nucleotide diversity and strong population structure, with the presence of two major clades corresponding to ecological origins (cheese and kefir vs. plant derivatives). A high prevalence of extensive loss of heterozygosity and a slow linkage disequilibrium decay suggested a predominantly clonal mode of reproduction. Phenotypic analyses revealed growth variation under stress conditions, including high salinity and low pH, but no definitive link between phenotypic traits and environmental adaptation was established.","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/PMC11974382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691624","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 physiology of an engineered Saccharomyces cerevisiae strain that carries both an improved glycerol-3-phosphate and the synthetic dihydroxyacetone pathway for glycerol utilization.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf015

Andreea Perpelea, Frederico Mendonça Bahia, Joeline Xiberras, Putu Virgina Partha Devanthi, Paola Branduardi, Mathias Klein, Elke Nevoigt

{"title":"The physiology of an engineered Saccharomyces cerevisiae strain that carries both an improved glycerol-3-phosphate and the synthetic dihydroxyacetone pathway for glycerol utilization.","authors":"Andreea Perpelea, Frederico Mendonça Bahia, Joeline Xiberras, Putu Virgina Partha Devanthi, Paola Branduardi, Mathias Klein, Elke Nevoigt","doi":"10.1093/femsyr/foaf015","DOIUrl":"10.1093/femsyr/foaf015","url":null,"abstract":"Our laboratory previously established variants of the Saccharomyces cerevisiae strain CEN.PK113-1A able to grow in synthetic glycerol medium. One approach focused on improving the endogenous l-glycerol-3-phosphate (G3P) pathway, while a second approach aimed to replace the endogenous pathway with the dihydroxyacetone (DHA) pathway. The latter approach led to a significantly higher maximum specific growth rate (µmax) of 0.26 h-1 compared to 0.14 h-1. The current study focused on combining all genetic modifications in one strain. Apart from the so-called \"TWO pathway strain\" (CEN TWOPW), two isogenic control strains, CEN G3PPW and CEN DHAPW, were constructed. The µmax of CEN TWOPW (∼0.24 h-1) was virtually identical to that of CEN DHAPW. Remarkable characteristics of the strain CEN TWOPW compared to CEN DHAPW include a higher specific glycerol consumption rate, the capacity to deplete glycerol completely, and a much higher ethanol and lower biomass formation during oxygen-limited shake flask cultivations. The results obtained with different alleles of the GUT1 gene, encoding for glycerol kinase, suggest that the phenotype of the strain CEN TWOPW is at least partly attributed to the particular point mutation in the GUT1 allele used from the strain JL1, which was previously generated through adaptive laboratory evolution.","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/PMC11974383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751853","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

Exploring pectinolytic yeast diversity: toward effective polygalacturonase producers for applications in wine-making. 探索果胶分解酵母菌的多样性：寻找在酿酒中应用的有效的聚半乳糖醛酸酶生产者。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foae033

Mehmet Gazaloğlu, Carole Camarasa, Elke Nevoigt

{"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":"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.","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}

引用次数: 0

Cdr1 in focus: a personal reflection on multidrug transporter research.

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

Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices.

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

Aging research has lost a brilliant investigator-Michael Breitenbach, 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

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.

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