FEMS yeast research最新文献

Genetic and phenotypic diversity of wine-associated Hanseniaspora species. 葡萄酒相关菌的遗传和表型多样性。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-06-11 DOI: 10.1093/femsyr/foaf031

Cristobal A Onetto, Chris Ward, Cristian Varela, Laura Hale, Simon A Schmidt, Anthony Borneman

{"title":"Genetic and phenotypic diversity of wine-associated Hanseniaspora species.","authors":"Cristobal A Onetto, Chris Ward, Cristian Varela, Laura Hale, Simon A Schmidt, Anthony Borneman","doi":"10.1093/femsyr/foaf031","DOIUrl":"https://doi.org/10.1093/femsyr/foaf031","url":null,"abstract":"The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow- (SEL) and fast-evolving lineages (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 113 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265815","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

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing. 面向可持续生物制造的红圆菌木糖代谢途径工程。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-06-11 DOI: 10.1093/femsyr/foaf029

Hyunjoon Oh, Hyun Gi Koh, Suk-Chae Jung, Qaunhui Ye, Sujit Sadashiv Jagtap, Christopher V Rao, Yong-Su Jin

{"title":"Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing.","authors":"Hyunjoon Oh, Hyun Gi Koh, Suk-Chae Jung, Qaunhui Ye, Sujit Sadashiv Jagtap, Christopher V Rao, Yong-Su Jin","doi":"10.1093/femsyr/foaf029","DOIUrl":"https://doi.org/10.1093/femsyr/foaf029","url":null,"abstract":"The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265814","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

The experimentally evolved fluconazole-resistant Clade II isolates of Candidozyma auris exhibit a distinct lipid compositional landscape, highlighting intra-clade sphingolipid heterogeneity. 实验进化的抗氟康唑进化枝II型耳念珠菌分离株表现出独特的脂质组成景观，突出了进化枝内鞘脂的异质性。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-05-30 DOI: 10.1093/femsyr/foaf030

Praveen Kumar, Basharat Ali, Mohit Kumar, Hans Carolus, Celia Lobo Romero, Rudy Vergauwen, Anshu Chauhan, Aswathy Narayanan, Atanu Banerjee, Naseem A Gaur, Ashutosh Singh, Patrick Van Dijck, Arunaloke Chakrabarti, Shiva Prakash M Rudramurthy, Kaustuv Sanyal, Rajendra Prasad

{"title":"The experimentally evolved fluconazole-resistant Clade II isolates of Candidozyma auris exhibit a distinct lipid compositional landscape, highlighting intra-clade sphingolipid heterogeneity.","authors":"Praveen Kumar, Basharat Ali, Mohit Kumar, Hans Carolus, Celia Lobo Romero, Rudy Vergauwen, Anshu Chauhan, Aswathy Narayanan, Atanu Banerjee, Naseem A Gaur, Ashutosh Singh, Patrick Van Dijck, Arunaloke Chakrabarti, Shiva Prakash M Rudramurthy, Kaustuv Sanyal, Rajendra Prasad","doi":"10.1093/femsyr/foaf030","DOIUrl":"https://doi.org/10.1093/femsyr/foaf030","url":null,"abstract":"The intrinsic resistance of Candidozyma auris to antifungal drugs poses a major therapeutic challenge, with conventional resistance mechanisms providing only partial explanations. Sphingolipids (SLs), known for their interclade heterogeneity, play a crucial role in antifungal resistance. This study examined the SL landscape in two drug-susceptible clade II isolates, C-line and P-line, from distinct geographical origins, which were experimentally evolved to develop stable fluconazole (FLC) resistance. The progenitors displayed distinct SL profiles, P1 had higher PhytoCer and αOHPhytoCer, indicating a more active acidic SL biosynthesis branch, whereas C1 exhibited elevated αOHGlcCer, αOHCer, and LCBs, reflecting a greater role of the neutral biosynthesis branch. The principal component analysis (PCA) also confirmed distinct segregation of the two progenitors. Upon evolution, P1.1 and C1.1 adaptors showed significant SL alterations. P1.1 exhibited PhytoCer enrichment, while C1.1 showed reduced αOHGlcCer alongside increased PhytoCer, dhCer and αOHPhytoCer levels. Notably, αOHGlcCer remained unchanged in P1.1, whereas LCBs and αOHPhytoCer decreased compared to P1. Despite these lineage-specific differences between the progenitors, both evolved replicates exhibited increased PhytoCer as a common denominator like what is also observed in clinical FLC-resistant isolates. These findings highlight intra-clade SL variability and suggest that specific SLs contribute to FLC resistance in C. auris.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186898","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

Molecular Evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts. 半真菌酵母中Pdr转运体Snq2/Pdr18亚家族成员的分子进化

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-05-27 DOI: 10.1093/femsyr/foaf026

Paulo Jorge Dias

{"title":"Molecular Evolution of the members of the Snq2/Pdr18 subfamily of Pdr transporters in the Hemiascomycete yeasts.","authors":"Paulo Jorge Dias","doi":"10.1093/femsyr/foaf026","DOIUrl":"https://doi.org/10.1093/femsyr/foaf026","url":null,"abstract":"The transporters of the ATP-Binding Cassette (ABC) Superfamily involved in the Multidrug Resistance (MDR) phenomena are also known as ABC Pleiotropic Drug Resistance (PDR) proteins. The homologs of the Saccharomyces cerevisiae SNQ2 and PDR18 genes were identified in 171 yeast genomes, representing 68 different hemiascomycetous species. All early-divergent yeast species analyzed in this work lack Snq2/Pdr18 homologs, suggesting that the origin of these ABC-PDR genes in hemiascomycete yeasts resulted from a horizontal transfer event. The evolutionary pathway of the Snq2/Pdr18 protein subfamily in pathogenic Candida species was also reconstructed, revealing a main gene lineage leading to the C. albicans SNQ2 gene. The results indicate that, after the gene duplication event at the origin of the SNQ2/PDR18 paralogs, the PDR18 ortholog has been under strong diversifying selection and suggest that a small portion of the sequence of the SNQ2 ancestral ortholog might have been under mild positive selection. The results also showed that strong positive selection was exerted over one of the two paralogs generated by the Whole Genome Duplication (WGD) event, corresponding to the duplicate at the origin of a \"short-lived\" WGD sublineage.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144157638","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. Crabtree阴性酿酒酵母的制备进展及其在化工生物合成中的应用。

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

Recent advances in genetic engineering and chemical production in yeast species. 酵母类基因工程和化学生产的最新进展。

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

Integrated omic analysis of a new flavor yeast strain in fermented rice milk. 一株发酵米浆风味酵母的综合组学分析。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 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":"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":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11995695/pdf/","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Experimental evolution and hybridization enhance the fermentative capacity of wild Saccharomyces eubayanus strains. 实验进化和杂交提高真芽酵母菌野生菌株的发酵能力。

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. 从火龙果中提取的BAHD酰基转移酶可以在工程酵母中产生叶根肌动蛋白。

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