FEMS yeast research最新文献

Regulation of meiotic gene expression is functional in the human fungal pathogen Candida glabrata.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-04-02 DOI: 10.1093/femsyr/foaf018

Natalia Klimova, Cindy Ngov, Frédéric Devaux, Bernard Turcotte

{"title":"Regulation of meiotic gene expression is functional in the human fungal pathogen Candida glabrata.","authors":"Natalia Klimova, Cindy Ngov, Frédéric Devaux, Bernard Turcotte","doi":"10.1093/femsyr/foaf018","DOIUrl":"https://doi.org/10.1093/femsyr/foaf018","url":null,"abstract":"The human fungal pathogen Candida glabrata is closely related to the budding yeast Saccharomyces cerevisiae. The sexual cycle in S. cerevisiae has been extensively characterized. Haploid cells 'a' and alpha secrete pheromones involved in mating of the opposite cell type leading to the formation of a diploid cell. Under harsh conditions, diploid cells undergo meiosis for the formation of four haploid spores. In C. glabrata, cells are also found as 'a' and alpha and this organism possesses most S. cerevisiae homologous genes involved in meiosis and mating. However, mating has never been observed in C. glabrata. In S. cerevisiae, the non-essential UME6 gene is involved in controlling the expression of meiotic genes. We have previously shown that Zcf11, a putative homolog of Ume6, is encoded by an essential gene but its function is unknown. Here we show that the expression of UME6 in C. glabrata can partially complement a Zcf11 knock-down and that these factors recognize the same DNA sequence Importantly, expression profiling using a Zcf11 knock-down strain revealed that this factor is a negative regulator of meiotic genes expression as well as some genes involved in mating. Thus, regulation of the expression of meiotic genes is functional in this organism reinforcing the view that C. glabrata may have a sexual cycle under specific conditions.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143771812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated omic analysis of a new flavor yeast strain in fermented rice milk.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-03-27 DOI: 10.1093/femsyr/foaf017

Chayaphathra Sooklim, Atchara Paemanee, Khanok Ratanakhanokchai, Duanghathai Wiwatratana, Nitnipa Soontorngun

{"title":"Integrated omic analysis of a new flavor yeast strain in fermented rice milk.","authors":"Chayaphathra Sooklim, Atchara Paemanee, Khanok Ratanakhanokchai, Duanghathai Wiwatratana, Nitnipa Soontorngun","doi":"10.1093/femsyr/foaf017","DOIUrl":"https://doi.org/10.1093/femsyr/foaf017","url":null,"abstract":"Plant-based milk contains high nutritional value with enriched vitamins, minerals, and essential amino acids. This study aimed to enhance the biochemical and biological properties of rice milk through yeast fermentation, using the novel fermenting strain Saccharomyces cerevisiae RSO4, which has superb fermenting ability for an innovative functional beverage. An integrated omics approach identified specific genes that exhibited genetic variants related to various cellular processes, including flavor and aroma production (ARO10, ADH1-5, and SFA1), whereas the proteomic profiles of RSO4 identified key enzymes whose expression was upregulated during fermentation of cooked rice, including the enzymes in glycogen branching (Glc3), glycolysis (Eno1, Pgk1 and Tdh1/2), stress response (Hsp26 and Hsp70), amino acid metabolism, and cell wall integrity. Biochemical and metabolomic analyses of the fermented rice milk by the RSO4 strain using the two rice varieties, Homali (Jasmine) white rice or Riceberry colored rice, detected differentially increased levels of bioactive compounds, such as β-glucan, vitamins, di-, and tripeptides, as well as pleasant flavors and aromas. The results of this study highlight the importance of selecting an appropriate fermenting yeast strain and rice variety to improve property of plant-based products as innovative functional foods.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735674","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","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 : 2025-03-20 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":"https://doi.org/10.1093/femsyr/foaf013","url":null,"abstract":"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 non-conventional 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":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel method for telomere length detection in fission yeast. 裂变酵母端粒长度检测的新方法。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foae040

Hadeel A B Elnaim Mohamed, Hizlan Hincal Agus, Bedia Palabiyik

{"title":"A novel method for telomere length detection in fission yeast.","authors":"Hadeel A B Elnaim Mohamed, Hizlan Hincal Agus, Bedia Palabiyik","doi":"10.1093/femsyr/foae040","DOIUrl":"10.1093/femsyr/foae040","url":null,"abstract":"Fission yeast is the ideal model organism for studying telomere maintenance in higher eukaryotes. Telomere length has been directly correlated with life expectancy and the onset of aging-related diseases in mammals. In this study, we developed a novel simple, and reproducible method to measure the telomere length, by investigating the effect of caffeine and cisplatin on the telomere length in fission yeast. Hydroxyurea-synchronized fission yeast cells were exposed to 62 µM cisplatin and 8.67 mM caffeine treatments for 2 h, then their telomere lengths were evaluated with two different methods. First, the quantitative polymerase chain reaction (qPCR) assay was used as a confirmative method, where telomere length was determined relative to a single-copy gene in the genome. Second, the newly developed method standard polymerase chain reaction (PCR)/ImageJ assay assessed the telomere length based on the amplified PCR band intensity using a set of telomere primers, reflecting telomeric sequence availability in the genome. Both methods show a significant decrease and a notable telomere lengthening in response to cisplatin and caffeine treatments, respectively. The finding supports the accuracy and productivity of the standard PCR/ImageJ assay as it can serve as a quick screening tool to study the effect of suspected chemotherapeutic and antiaging drugs on telomere length in fission yeast.","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/PMC11781191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885275","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 advances in creating Crabtree-negative Saccharomyces cerevisiae and the application for chemicals biosynthesis.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf014

Yalin Guo, Zhen Xiong, Haotian Zhai, Yuqi Wang, Qingsheng Qi, Jin Hou

引用次数: 0

Experimental evolution and hybridization enhance the fermentative capacity of wild Saccharomyces eubayanus strains.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf004

Franco Vega-Macaya, Pablo Villarreal, Tomas A Peña, Valentina Abarca, Agustín A Cofré, Christian I Oporto, Wladimir Mardones, Roberto F Nespolo, Francisco A Cubillos

{"title":"Experimental evolution and hybridization enhance the fermentative capacity of wild Saccharomyces eubayanus strains.","authors":"Franco Vega-Macaya, Pablo Villarreal, Tomas A Peña, Valentina Abarca, Agustín A Cofré, Christian I Oporto, Wladimir Mardones, Roberto F Nespolo, Francisco A Cubillos","doi":"10.1093/femsyr/foaf004","DOIUrl":"10.1093/femsyr/foaf004","url":null,"abstract":"Lager beer is traditionally fermented using Saccharomyces pastorianus. However, the limited availability of lager yeast strains restricts the potential range of beer profiles. Recently, Saccharomyces eubayanus strains showed the potential to impart novel aromas to beer, with slower fermentation rates than commercial strains. Here, we applied experimental evolution to nine S. eubayanus strains using three different selective conditions to generate improved strains to fermentative environments. We observed environment-dependent fitness changes across strains, with ethanol-enriched media resulting in the greatest fitness improvement. We identified subtelomeric genomic changes in a deficient fermentative strain underlying the greatest fitness improvement. Gene expression analysis and genome sequencing identified genes associated with oxidative stress, amino acid metabolism, sterol biosynthesis, and vacuole morphology underlying differences between evolved and the ancestral strain, revealing the cellular processes underlying fermentation improvement. A hybridization strategy between two evolved strains allowed us to expand the phenotypic space of the F2 segregants, obtaining strains with a 13.7% greater fermentative capacity relative to the best evolved parental strains. Our study highlights the potential of integrating experimental evolution and hybridization to enhance the fermentation capacity of wild yeast strains, offering strengthened solutions for industrial applications and highlighting the potential of Patagonian S. eubayanus in brewing.","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/PMC11878536/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143064865","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

BAHD acyltransferase from dragon fruit enables production of phyllocactin in engineered yeast.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foae041

Christiane Glitz, Jane Dannow Dyekjær, Sophia Mattitsch, Mahsa Babaei, Irina Borodina

{"title":"BAHD acyltransferase from dragon fruit enables production of phyllocactin in engineered yeast.","authors":"Christiane Glitz, Jane Dannow Dyekjær, Sophia Mattitsch, Mahsa Babaei, Irina Borodina","doi":"10.1093/femsyr/foae041","DOIUrl":"10.1093/femsyr/foae041","url":null,"abstract":"Microbial fermentation can provide a sustainable and cost-effective alternative to traditional plant extraction to produce natural food colours. Betalains are a class of yellow to red water-soluble pigments. Even though over 80 betalain variants are known, betanin is the only betalain available as a food colourant on the market. Many variants are acylated, which can enhance their stability and change the hue, but very few acyltransferases responsible for the acylation are known. Therefore, we mined the transcriptomes of Celosia argentea var. cristata and Hylocereus polyrhizus for BAHD acyltransferases, enzymes likely involved in betalain acylation. In vivo screening of the enzymes in betanin-producing Saccharomyces cerevisiae revealed that the acyltransferase HpBAHD3 from H. polyrhizus malonylates betanin, forming phyllocactin (6'-O-malonyl-betanin). This is the first identification of a BAHD acyltransferase involved in betalain biosynthesis. Expression of HpBAHD3 in a Yarrowia lipolytica strain engineered for high betanin production led to near-complete conversion of betanin to phyllocactin. In fed-batch fermentation, the strain produced 1.95 ± 0.024 g/l phyllocactin in 60 h. This study expands the range of natural food colourants produced through microbial fermentation and contributes to elucidating the biosynthesis pathway of acylated betalains.","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/PMC11881927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143390432","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

Recent advances in genetic engineering and chemical production in yeast species.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf009

Sangdo Yook, Hal S Alper

引用次数: 0

Characterizing heterologous protein burden in Komagataella phaffii.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf007

Louise La Barbera Kastberg, Irene Hjorth Jacobsen, Emre Özdemir, Christopher T Workman, Michael Krogh Jensen, Jochen Förster

{"title":"Characterizing heterologous protein burden in Komagataella phaffii.","authors":"Louise La Barbera Kastberg, Irene Hjorth Jacobsen, Emre Özdemir, Christopher T Workman, Michael Krogh Jensen, Jochen Förster","doi":"10.1093/femsyr/foaf007","DOIUrl":"10.1093/femsyr/foaf007","url":null,"abstract":"Yeast is a widely utilized chassis for heterologous protein production, with Komagataella phaffii well-established as a prominent nonconventional yeast in this field. Despite its widespread recognition, there remains considerable potential to further optimize these cell factories to meet high production demands in a cost-effective and sustainable manner. Understanding the cellular response to the challenges of heterologous protein production can equip genetic engineers with crucial knowledge to develop enhanced strategies for constructing more efficient cell factories. In this study, we explore the molecular response of various K. phaffii strains that produce either the human insulin precursor or Mambalgin-1, examining changes in transcription and changes in intra- and extracellular protein levels. Our findings provide valuable insights into the molecular mechanisms that regulate the behaviour of K. phaffii production strains under the stress of producing different heterologous proteins. We believe that these results will serve as a foundation for identifying new genetic targets to improve strain robustness and productivity. In conclusion, we present new cellular and molecular insights into the response of K. phaffii cell factories to the challenges of burdensome heterologous protein production and our findings point to different engineering strategies for improved cell factory performance.","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/PMC11881926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143457331","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

Challenges in elucidating ethylene glycol metabolism in Saccharomyces cerevisiae.

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf006

Vittorio Giorgio Senatore, Fiorella Masotti, Riccardo Milanesi, Sofia Ceccarossi, Letizia Maestroni, Immacolata Serra, Paola Branduardi

{"title":"Challenges in elucidating ethylene glycol metabolism in Saccharomyces cerevisiae.","authors":"Vittorio Giorgio Senatore, Fiorella Masotti, Riccardo Milanesi, Sofia Ceccarossi, Letizia Maestroni, Immacolata Serra, Paola Branduardi","doi":"10.1093/femsyr/foaf006","DOIUrl":"10.1093/femsyr/foaf006","url":null,"abstract":"Polyethylene terephthalate (PET) is one of the most used polymers in the packaging industry; enzymatic recycling is emerging as a sustainable strategy to deal with waste PET, producing the virgin monomers terephthalic acid and ethylene glycol (EG). These monomers can be feedstocks for further microbial transformations. While EG metabolism has been uncovered in bacteria, in yeast the pathway for the oxidation to glycolic acid (GA) has only been proposed, but never experimentally elucidated. In this work, we investigated in Saccharomyces cerevisiae the potential contribution to this metabolism of two endogenous genes, YLL056C (a putative alcohol dehydrogenase) and GOR1 (glyoxylate reductase). Secondly, the possible role of alcohol dehydrogenases (ADHs) was considered, too. Finally, two heterologous genes (gox0313 from Gluconobacter oxydans and AOX1 from Komagataella phaffii) were expressed with the intent to push EG oxidation toward GA. Our main findings revealed that (i) Gor1, Yll056c, and ADHs are not involved in EG oxidation and (ii) the bottleneck of the catabolism is the first step in the pathway, due to the endogenous mechanisms for aldehyde detoxification. Multiomics studies are required to completely elucidate the pathway for EG catabolism, while further engineering directed toward relieving the bottleneck is needed to fully unleash the potential of yeasts for the upcycling of EG to GA.","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/PMC11878538/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370485","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