FEMS yeast research最新文献_第3页

A CRISPR/Cas9-based genome-editing platform enabling efficient and precise gene replacement in Lipomyces starkeyi. 一种基于CRISPR/ cas9的基因组编辑平台，可在starkeyi脂菌中实现高效和精确的基因替换。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag014

Rikako Sato, Kaito Maruyama, Satoshi Ara, Masayuki Shibata, Yosuke Shida, Wataru Ogasawara, Harutake Yamazaki, Hiroaki Takaku

{"title":"A CRISPR/Cas9-based genome-editing platform enabling efficient and precise gene replacement in Lipomyces starkeyi.","authors":"Rikako Sato, Kaito Maruyama, Satoshi Ara, Masayuki Shibata, Yosuke Shida, Wataru Ogasawara, Harutake Yamazaki, Hiroaki Takaku","doi":"10.1093/femsyr/foag014","DOIUrl":"10.1093/femsyr/foag014","url":null,"abstract":"Lipomyces starkeyi is a promising oleaginous yeast with industrial potential. However, its genome engineering remains constrained by low gene-targeting efficiency and the requirement for long homologous regions. Herein, we established a CRISPR/Cas9 genome-editing platform for L. starkeyi by expressing codon-optimized Streptococcus pyogenes Cas9 fused to an SV40 nuclear localization signal. Furthermore, in vitro-transcribed single-guide RNAs (sgRNAs) were directly delivered into the host, eliminating the need for endogenous RNA polymerase III-dependent sgRNA expression. CRISPR/Cas9 activity was validated using a codon-optimized Aequorea coerulescens GFP reporter. Cas9-induced frameshift mutations caused GFP disruption, leading to fluorescence loss. Gene replacement at the LsURA3 locus was evaluated using donor constructs with homologous regions ranging from 50-3000 bp. In a Cas9-expressing wild-type background, precise gene replacement was dependent on homology arm length, increasing from 36% with 50-bp arms to 80% with 3000-bp arms. Notably, in a Cas9-expressing Δlslig4 strain with suppressed non-homologous end joining (NHEJ), precise gene replacement was achieved with 100% accuracy using 50-bp homology arms under CRISPR/Cas9-dependent conditions. Together, these results demonstrate that a Pol III-independent CRISPR/Cas9 system combined with NHEJ suppression enables precise genome editing in L. starkeyi, providing a foundation for functional genomics and metabolic engineering.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13159722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147766849","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

Establishment of a protoplast transformation method for the oleaginous yeast Rhodotorula toruloides. 产油酵母原生质体转化方法的建立。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag028

Xin Chen, Verena Siewers

{"title":"Establishment of a protoplast transformation method for the oleaginous yeast Rhodotorula toruloides.","authors":"Xin Chen, Verena Siewers","doi":"10.1093/femsyr/foag028","DOIUrl":"10.1093/femsyr/foag028","url":null,"abstract":"Rhodotorula toruloides is an oleaginous yeast with great potential for chemical and biofuel production, due to its ability to utilize lignocellulosic biomass and to produce high levels of carotenoids and storage lipids. However, its broader application in biotechnology has been limited by the lack of efficient genetic transformation methods. Although protoplast transformation is wildly used in fungal systems, it has remained largely unexplored in R. toruloides. In this study, we established a protoplast transformation protocol using linear DNA fragments and R. toruloides strain BOT-A2, a recently isolated strain with high lipid-producing potential. We first confirmed that BOT-A2 is a MAT A2 haploid strain. We then produced a β-1,3-glucomannanase (Man5C) that effectively digests the R. toruloides cell wall. Key parameters affecting transformation efficiency were systematically optimized, including the Man5C digestion conditions, antibiotic selection pressure, cell growth phase, protoplast yield and viability, PEG formulation, calcium ion concentration, and regeneration conditions. Using the optimized protocol, we successfully transformed BOT-A2 with three heterologous resistance cassettes (hygromycin R, bleomycin, and G418) yielding 190, 226, and 244 transformants per µg of DNA, respectively. This method provides a platform for genetic manipulation and is expected to facilitate both fundamental research and metabolic engineering in R. toruloides BOT-A2.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13343485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148338375","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

Saccharomyces cerevisiae as a model for mammalian diseases. 作为哺乳动物疾病模型的酿酒酵母菌。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag013

Evelyn Sattlegger, Anja H Schiemann

{"title":"Saccharomyces cerevisiae as a model for mammalian diseases.","authors":"Evelyn Sattlegger, Anja H Schiemann","doi":"10.1093/femsyr/foag013","DOIUrl":"10.1093/femsyr/foag013","url":null,"abstract":"For many human diseases and disorders, the underlying molecular mechanism often remains poorly understood, limiting progress in developing effective targeted therapies and diagnostic tools. To fill this gap in knowledge, surrogate systems are required that faithfully recapitulate in vivo biology, as direct experimentation in humans is not feasible. Most mammalian cell lines are immortalized and genetically altered, making them limited representatives of normal physiological states. Animal models are costly, labour-intensive, and raise ethical concerns. On the other hand, the eukaryote Saccharomyces cerevisiae is a powerful model system for deciphering biological mechanisms and diseases in exquisite molecular detail. Fundamental cellular and molecular processes are highly conserved between yeast and humans. Yeast can be diploid, or haploid where the effect of a genetic change is not masked by the intact second allele. It is inexpensive to handle, grows rapidly, and is highly amenable to manipulation at the genetic, molecular, biochemical, and cellular level. Moreover, an ever-growing array of advanced technologies, protocols, yeast collections and libraries, and databases is available. This review highlights examples in which yeast has advanced our understanding of biological processes and diseases, facilitated drug development, and informed therapeutic interventions, demonstrating that it remains highly relevant in modern biomedical research.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13094546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147503512","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

Yeasts in the gastrointestinal tract. 胃肠道中的酵母菌。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag029

Katherine D Mueller, Soo Chan Lee

引用次数: 0

Systems biology of yeast metabolism. 酵母代谢系统生物学。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag026

Jens Nielsen

{"title":"Systems biology of yeast metabolism.","authors":"Jens Nielsen","doi":"10.1093/femsyr/foag026","DOIUrl":"10.1093/femsyr/foag026","url":null,"abstract":"Metabolism underpins cellular function by supplying energy, biosynthetic precursors, and redox balance and in yeast there are thousands of metabolic reactions that are tightly coordinated through multilayered regulation. The yeast Saccharomyces cerevisiae has become a central model for studying metabolism and its regulation and following publication of its genome in 1996, this yeast became pivotal in systems biology. Systems biology integrates experimental data with mathematical modeling to analyse complex cellular networks. A major advance for metabolic analysis was the development of flux balance analysis and genome sequencing enabled reconstruction of the first genome-scale metabolic model (GEM) for yeast. This initial GEM described how hundreds of genes, reactions, and metabolites interact across compartments. Subsequent models, including Yeast8 and Yeast9, expanded the coverage and predictive power, and these models enable metabolic comparison, physiological analysis, omics integration, and design of strains that can be used for production of chemicals and biopharmaceuticals. Overall, S. cerevisiae remains a cornerstone of systems biology and biotechnology, with continued advances expected in integrative modeling and engineering applications.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13296557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257967","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

Transcriptional regulation: efficient genetic engineering tools for non-conventional yeasts. 转录调控：非常规酵母的高效基因工程工具。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag032

Shabana Haneef, Yongjin J Zhou, Fan Bai

{"title":"Transcriptional regulation: efficient genetic engineering tools for non-conventional yeasts.","authors":"Shabana Haneef, Yongjin J Zhou, Fan Bai","doi":"10.1093/femsyr/foag032","DOIUrl":"10.1093/femsyr/foag032","url":null,"abstract":"Non-conventional yeasts are recognized as valuable hosts for producing biofuels, pharmaceuticals, and other high-value chemicals, owing to their diverse physiological traits, ability to utilize various substrates, and greater tolerance to environmental stresses compared to conventional model yeast Saccharomyces cerevisiae. To fully optimizing metabolic flux toward desired products, effective genetic engineering tools enabling precise modulation of gene expression and coordinated control of metabolic pathways are essential. In this context, we discussed classical transcriptional regulation tools like promoters, and transcription factors, alongside innovations in synthetic biology that allow metabolic engineering in non-conventional yeasts to produce higher biofuels and other useful products, promoting the development of sustainable resources, and assisting the development of innovative bio-products. It also discussed innovative programmable technologies, such as CRISPR/Cas-mediated transcriptional activation and repression, as well as dynamic regulatory systems that can fine-tune metabolic routes and balance cellular resources. Strategies for promoter engineering, transcription factor manipulation for transcriptional regulation, and metabolic rewiring were highlight as methods to boost pathway efficiency and yields. This review concluded with current challenges and future directions, focusing on integrating synthetic biology and systems biology to create robust, controllable transcriptional frameworks for next-generation yeast cell factories.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668583","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

Life beyond 6000 genes: from sequence to synthesis in a post-genomics era. 超过6000个基因的生命：后基因组时代从序列到合成。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag034

Roy S K Walker, Edward Archer, Paige Erpf, Ian T Paulsen, Isak S Pretorius

{"title":"Life beyond 6000 genes: from sequence to synthesis in a post-genomics era.","authors":"Roy S K Walker, Edward Archer, Paige Erpf, Ian T Paulsen, Isak S Pretorius","doi":"10.1093/femsyr/foag034","DOIUrl":"10.1093/femsyr/foag034","url":null,"abstract":"The publication of the Saccharomyces cerevisiae genome sequence thirty years ago marked a defining shift in modern biology, establishing yeast as the first fully sequenced eukaryotic model cell. Access to a complete reference genome has catalyzed a renaissance in experimental biology, providing the foundation for advances in functional genomics, systems biology, synthetic biology, and biotechnology. This article celebrates the achievements of the yeast sequencing project and highlights how genomics has evolved from a descriptive resource into a central enabling infrastructure for engineering biology, leading to a post-genomic era defined by genome-scale design. We chart the progression from decoding the genome to the omics revolution, highlighting both recent discoveries and persistent enigmas surrounding the 'dark matter' of the yeast genome. We then describe how access to a well-annotated reference genome has culminated in a new era of synthetic genomics exemplified by the Sc2.0 project. Finally, we explore how emerging trends in artificial intelligence and bioelectronics may shape the next thirty years of yeast genomics and engineering biology. This integration of past achievements and future trajectories reinforces the enduring role of S. cerevisiae as a primary eukaryotic model for biological discovery and biotechnological innovation.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459950/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148677788","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

Indigenous microorganisms and benefit sharing. 本土微生物与惠益分享。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag016

Katie Lee Riddle, Rogena Sterling, Maui Hudson, Jane Anderson

引用次数: 0

De novo genome assembly of a native Saccharomyces cerevisiae strain isolated from spontaneous fermentation of vineyard must in the Atacama Desert (Chile). 智利阿塔卡马沙漠葡萄自发发酵中分离的一株酿酒酵母菌的基因组组装。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag033

Héctor Aguayo-Cumplido, Michelle Cifras-Céspedes, Marcelo Lanino, Ingrid Poblete, Jennifer Molinet, Lía Ramírez-Fernández

{"title":"De novo genome assembly of a native Saccharomyces cerevisiae strain isolated from spontaneous fermentation of vineyard must in the Atacama Desert (Chile).","authors":"Héctor Aguayo-Cumplido, Michelle Cifras-Céspedes, Marcelo Lanino, Ingrid Poblete, Jennifer Molinet, Lía Ramírez-Fernández","doi":"10.1093/femsyr/foag033","DOIUrl":"10.1093/femsyr/foag033","url":null,"abstract":"In this work, we investigated the genomic and phenotypic basis of stress tolerance in the native Saccharomyces cerevisiae strain M6, isolated from spontaneously fermenting must at a vineyard located in Atacama Desert, through a de novo hybrid genome assembly generated using short- and long-read sequencing technologies. The assembly comprised 11.89 Mb with high completeness (99.5%), and flow cytometry analysis confirmed a diploid genome organization. Phylogenomic analyses placed M6 within the Wine/European lineage, although displaying genomic divergence relative to other wine-associated strains. Using S288C as the reference genome, comparative variant analysis was performed for M6 and four closely related strains, including Wine/European and Alpechin strains. Coding variants were identified in genes associated with osmotic sensing and signaling (SSK1, SSK2), trehalose metabolism (TPS2, NTH1). Growth assays demonstrate that M6 exhibits enhanced performance under elevated temperatures (35°C-38°C) and high salinity (up to 1.5 M NaCl) compared with commercial and laboratory strains. In addition, Biolog YT assays revealed broad carbohydrate utilization capacity, including the metabolism of maltose, galactose, and raffinose-family oligosaccharides. Together, these results provide integrated genomic and phenotypic evidence of stress resistance and metabolic flexibility in strain M6, highlighting its potential as a biotechnological resource for fermentation processes.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13495792/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668435","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

Reprogramming a Hgt-family Kluyveromyces marxianus sugar transporter by site-directed mutagenesis to enable co-consumption of glucose and xylose. 通过位点定向诱变对hgh家族克卢维酵母糖转运蛋白进行重编程，使葡萄糖和木糖能够共同消耗。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2026-01-05 DOI: 10.1093/femsyr/foag035

Lorena Donzella, Carlos Belloch-Molina, John P Morrissey, Maria João Sousa

{"title":"Reprogramming a Hgt-family Kluyveromyces marxianus sugar transporter by site-directed mutagenesis to enable co-consumption of glucose and xylose.","authors":"Lorena Donzella, Carlos Belloch-Molina, John P Morrissey, Maria João Sousa","doi":"10.1093/femsyr/foag035","DOIUrl":"10.1093/femsyr/foag035","url":null,"abstract":"Efficient utilization of lignocellulosic hydrolysates in yeast-based biorefineries requires simultaneous consumption of glucose and xylose, which is often limited by preferential glucose uptake. In Kluyveromyces marxianus, we kinetically characterized two native xylose transporters, KMAR_10 531 and KMAR_60 179, identifying medium- and low-affinity xylose transporters, respectively. KMAR_10 531 also mediated high-affinity glucose uptake (Km 0.28 ± 0.1 mM), limiting xylose utilization in mixed-sugar media. Guided by structural modelling, we engineered the KMAR_10 531 N325V variant, which reduced glucose affinity ∼20-fold while improving xylose affinity more than three-fold (Km reduced from 46.9 ± 9.5 to 14.9 ± 3.6 mM). Expression of KMAR_10 531 N325V in a pentose-transporter-deficient K. marxianus strain enabled simultaneous glucose-xylose co-consumption in flasks and bioreactors, overcoming the diauxic growth observed with the native transporter. In bioreactors, the engineered strain consumed ∼90% of available xylose within 45 h and produced increased biomass compared to native transporter. This study provides the first example of engineering an Hgt-like transporter for altered sugar specificity.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2026-01-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13487788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148697242","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