FEMS yeast research最新文献_第10页

Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events. Cyberlindnera 酵母菌中 rDNA 基因的多态性提示了生死进化事件。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad032

Rodolfo Bizarria, Tatiane de Castro Pietrobon, Henrique Ferreira, Andre Rodrigues

{"title":"Polymorphisms of rDNA genes in Cyberlindnera yeast suggest birth-and-death evolution events.","authors":"Rodolfo Bizarria, Tatiane de Castro Pietrobon, Henrique Ferreira, Andre Rodrigues","doi":"10.1093/femsyr/foad032","DOIUrl":"10.1093/femsyr/foad032","url":null,"abstract":"In eukaryotes, the ribosome machinery is encoded by repeats of the ribosomal RNA genes: 26/28S, 18S, 5.8S, and 5S, structured in tandem arrays and frequently homogenized within a genome. This homogenization is thought to be driven by concerted evolution, evolving as a unit, which contributes to its target as the species barcode in modern taxonomy. However, high heterogeneity of rDNA genes has been reported, including in Saccharomycotina yeasts. Here, we describe the polymorphisms and heterogeneity of D1/D2 domains (26S rRNA) and the intergenic transcribed spacer of a new yeast species with affinities to the genus Cyberlindnera and their evolution. Both regions are not homogenized, failing the prediction of concerted evolution. Phylogenetic network analysis of cloned sequences revealed that Cyberlindnera sp. rDNAs are diverse and evolved by reticulation rather than by bifurcating tree evolution model. Predicted rRNA secondary structures also confirmed structural differences, except for some conserved hairpin loops. We hypothesize that some rDNA is inactive within this species and evolves by birth-and-death rather than concerted evolution. Our findings propel further investigation into the evolution of rDNA genes in yeasts.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"23 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9676026","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

Influence of different Lachancea thermotolerans strains in the wine profile in the era of climate challenge. 气候变化下不同耐温葡萄品种对葡萄酒品质的影响。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foac062

Javier Vicente, Niina Kelanne, Lydia Rodrigo-Burgos, Eva Navascués, Fernando Calderón, Antonio Santos, Domingo Marquina, Baoru Yang, Santiago Benito

{"title":"Influence of different Lachancea thermotolerans strains in the wine profile in the era of climate challenge.","authors":"Javier Vicente, Niina Kelanne, Lydia Rodrigo-Burgos, Eva Navascués, Fernando Calderón, Antonio Santos, Domingo Marquina, Baoru Yang, Santiago Benito","doi":"10.1093/femsyr/foac062","DOIUrl":"https://doi.org/10.1093/femsyr/foac062","url":null,"abstract":"The study performed sequential fermentations of red grape juice using several strains of Lachancea thermotolerans and one strain of Saccharomyces cerevisiae. Due to the new conditions imposed by climate change, wine acidity must be affected as well as the volatile profile. Non-Saccharomyces yeasts such as L. thermotolerans are real alternatives to soften the impact of climate change in winemaking. The L. thermotolerans strains included three commercially available strains and two wine-related natural isolates. L. thermotolerans showed significant statistical differences in basic chemical parameters such as lactic acid, malic acid, or ethanol concentrations as well as in the volatile profile. S. cerevisiae clearly produced some volatile compounds in higher amounts than the studied L. thermotolerans strains while others showed the opposite effect. Sequential fermentations involving any of the studied strains of L. thermotolerans with S. cerevisiae showed an increased volatile profile compared to the S. ceresisiae single fermentation, highlighting the synergic effect between the studied species.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"23 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10758485","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: 1

Optimizing the balance between heterologous acetate- and CO2-reduction pathways in anaerobic cultures of Saccharomyces cerevisiae strains engineered for low-glycerol production. 优化用于低甘油生产的酿酒酵母菌株厌氧培养中异源乙酸盐和CO2还原途径之间的平衡。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad048

Aafke C A van Aalst, Ellen H Geraats, Mickel L A Jansen, Robert Mans, Jack T Pronk

{"title":"Optimizing the balance between heterologous acetate- and CO2-reduction pathways in anaerobic cultures of Saccharomyces cerevisiae strains engineered for low-glycerol production.","authors":"Aafke C A van Aalst, Ellen H Geraats, Mickel L A Jansen, Robert Mans, Jack T Pronk","doi":"10.1093/femsyr/foad048","DOIUrl":"10.1093/femsyr/foad048","url":null,"abstract":"In anaerobic Saccharomyces cerevisiae cultures, NADH (reduced form of nicotinamide adenine dinucleotide)-cofactor balancing by glycerol formation constrains ethanol yields. Introduction of an acetate-to-ethanol reduction pathway based on heterologous acetylating acetaldehyde dehydrogenase (A-ALD) can replace glycerol formation as 'redox-sink' and improve ethanol yields in acetate-containing media. Acetate concentrations in feedstock for first-generation bioethanol production are, however, insufficient to completely replace glycerol formation. An alternative glycerol-reduction strategy bypasses the oxidative reaction in glycolysis by introducing phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). For optimal performance in industrial settings, yeast strains should ideally first fully convert acetate and, subsequently, continue low-glycerol fermentation via the PRK-RuBisCO pathway. However, anaerobic batch cultures of a strain carrying both pathways showed inferior acetate reduction relative to a strain expressing only the A-ALD pathway. Complete A-ALD-mediated acetate reduction by a dual-pathway strain, grown anaerobically on 50 g L-1 glucose and 5 mmol L-1 acetate, was achieved upon reducing PRK abundance by a C-terminal extension of its amino acid sequence. Yields of glycerol and ethanol on glucose were 55% lower and 6% higher, respectively, than those of a nonengineered reference strain. The negative impact of the PRK-RuBisCO pathway on acetate reduction was attributed to sensitivity of the reversible A-ALD reaction to intracellular acetaldehyde concentrations.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10647013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71520989","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

CRISPR-Cas9 engineering in the hybrid yeast Zygosaccharomyces parabailii can lead to loss of heterozygosity in target chromosomes. 在杂交酵母Zygosaccharomyces parabailii中进行CRISPR-Cas9工程可导致靶染色体的杂合性丧失。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad036

Pooja Jayaprakash, Liliane Barroso, Matteo Vajente, Letizia Maestroni, Edward J Louis, John P Morrissey, Paola Branduardi

{"title":"CRISPR-Cas9 engineering in the hybrid yeast Zygosaccharomyces parabailii can lead to loss of heterozygosity in target chromosomes.","authors":"Pooja Jayaprakash, Liliane Barroso, Matteo Vajente, Letizia Maestroni, Edward J Louis, John P Morrissey, Paola Branduardi","doi":"10.1093/femsyr/foad036","DOIUrl":"https://doi.org/10.1093/femsyr/foad036","url":null,"abstract":"The hybrid yeast Zygosaccharomyces parabailii holds potential as a cell factory mainly because of its robustness in withstanding stressors that often characterize bio-based processes. However, a complex genome and a lack of gene editing tools hinder the capacity to engineer this yeast. In this work, we developed a CRISPR-Cas9 gene editing system for Z. parabailii that allows simultaneous disruption or deletion of both alleles of a gene. We evaluated four different gRNA expression systems consisting of combinations of tRNAs, tRNA and ribozyme or ribozymes as self-cleaving flanking elements and established that the most efficient systems used an RNA Pol II promoter followed by a 5'tRNA flanking the gRNA. This gRNA system was then used to construct a strain of Z. parabailii in which both alleles of DNL4 were inactivated and so relied on homologous recombination to repair double-stranded breaks. Our system can be used for gene inactivation in a wild-type strain and precise deletion with marker insertion in a dnl4 mutant. In some cases, we observed inter-chromosomal recombination around the site of the DSB that could cause loss of heterozygosity through gene conversion or deletion. Although an additional aspect that needs to be monitored during strain engineering, this phenomenon also offers opportunities to explore genome plasticity in hybrid yeasts.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"23 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/41/2b/foad036.PMC10377752.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9892855","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

Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products. 韩国传统发酵酒精饮料和豆制品中酵母菌种的基因组和功能特征。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foac066

Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-Joo Jeon, Che Ok Jeon, Seong-Il Eyun, Hyun Ah Kang

{"title":"Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products.","authors":"Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-Joo Jeon, Che Ok Jeon, Seong-Il Eyun, Hyun Ah Kang","doi":"10.1093/femsyr/foac066","DOIUrl":"10.1093/femsyr/foac066","url":null,"abstract":"In this review, we describe the genomic and physiological features of the yeast species predominantly isolated from Nuruk, a starter for traditional Korean rice wines, and Jang, a traditional Korean fermented soy product. Nuruk and Jang have several prevalent yeast species, including Saccharomycopsis fibuligera, Hyphopichia burtonii, and Debaryomyces hansenii complex, which belong to the CUG clade showing high osmotic tolerance. Comparative genomics revealed that the interspecies hybridization within yeast species for generating heterozygous diploid genomes occurs frequently as an evolutional strategy in the fermentation environment of Nuruk and Jang. Through gene inventory analysis based on the high-quality reference genome of S. fibuligera, new genes involved in cellulose degradation and volatile aroma biosynthesis and applicable to the production of novel valuable enzymes and chemicals can be discovered. The integrated genomic and transcriptomic analysis of Hyphopichia yeasts, which exhibit strong halotolerance, provides insights into the novel mechanisms of salt and osmo-stress tolerance for survival in fermentation environments with a low-water activity and high-concentration salts. In addition, Jang yeast isolates, such as D. hansenii, show probiotic potential for the industrial application of yeast species beyond fermentation starters to diverse human health sectors.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"23 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9486864","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: 1

Metabolic reconstruction of the human pathogen Candida auris: using a cross-species approach for drug target prediction. 人类病原体耳念珠菌的代谢重建：使用跨物种方法预测药物靶点。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad045

Romeu Viana, Tiago Carreiro, Diogo Couceiro, Oscar Dias, Isabel Rocha, Miguel Cacho Teixeira

{"title":"Metabolic reconstruction of the human pathogen Candida auris: using a cross-species approach for drug target prediction.","authors":"Romeu Viana, Tiago Carreiro, Diogo Couceiro, Oscar Dias, Isabel Rocha, Miguel Cacho Teixeira","doi":"10.1093/femsyr/foad045","DOIUrl":"10.1093/femsyr/foad045","url":null,"abstract":"Candida auris is an emerging human pathogen, associated with antifungal drug resistance and hospital candidiasis outbreaks. In this work, we present iRV973, the first reconstructed Genome-scale metabolic model (GSMM) for C. auris. The model was manually curated and experimentally validated, being able to accurately predict the specific growth rate of C. auris and the utilization of several sole carbon and nitrogen sources. The model was compared to GSMMs available for other pathogenic Candida species and exploited as a platform for cross-species comparison, aiming the analysis of their metabolic features and the identification of potential new antifungal targets common to the most prevalent pathogenic Candida species. From a metabolic point of view, we were able to identify unique enzymes in C. auris in comparison with other Candida species, which may represent unique metabolic features. Additionally, 50 enzymes were identified as potential drug targets, given their essentiality in conditions mimicking human serum, common to all four different Candida models analysed. These enzymes represent interesting drug targets for antifungal therapy, including some known targets of antifungal agents used in clinical practice, but also new potential drug targets without any human homolog or drug association in Candida species.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49676115","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

Correction to: The prevalence of killer yeasts and double-stranded RNAs in the budding yeast Saccharomyces cerevisiae. 更正：芽殖酵母中致命酵母和双链 RNA 的普遍性。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad051

引用次数: 0

PCR-based gene targeting in Hanseniaspora uvarum. 基于pcr的兔痘菌基因靶向研究。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad034

Jennifer Badura, Niël van Wyk, Kerstin Zimmer, Isak S Pretorius, Christian von Wallbrunn, Jürgen Wendland

{"title":"PCR-based gene targeting in Hanseniaspora uvarum.","authors":"Jennifer Badura, Niël van Wyk, Kerstin Zimmer, Isak S Pretorius, Christian von Wallbrunn, Jürgen Wendland","doi":"10.1093/femsyr/foad034","DOIUrl":"https://doi.org/10.1093/femsyr/foad034","url":null,"abstract":"Lack of gene-function analyses tools limits studying the biology of Hanseniaspora uvarum, one of the most abundant yeasts on grapes and in must. We investigated a rapid PCR-based gene targeting approach for one-step gene replacement in this diploid yeast. To this end, we generated and validated two synthetic antibiotic resistance genes, pFA-hygXL and pFA-clnXL, providing resistance against hygromycin and nourseothricin, respectively, for use with H. uvarum. Addition of short flanking-homology regions of 56-80 bp to these selection markers via PCR was sufficient to promote gene targeting. We report here the deletion of the H. uvarum LEU2 and LYS2 genes with these marker genes via two rounds of consecutive transformations, each resulting in the generation of auxotrophic strains (leu2/leu2; lys2/lys2). The hereby constructed leucine auxotrophic leu2/leu2 strain was subsequently complemented in a targeted manner, thereby further validating this approach. PCR-based gene targeting in H. uvarum was less efficient than in Saccharomyces cerevisiae. However, this approach, combined with the availability of two marker genes, provides essential tools for directed gene manipulations in H. uvarum.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"23 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10172564","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: 1

Current trends and future perspective of probiotic yeasts research in Indonesia. 印尼益生菌研究现状及未来展望

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foad013

Rika Indri Astuti, Muhammad Eka Prastya, Rahayu Wulan, Khairul Anam, Anja Meryandini

{"title":"Current trends and future perspective of probiotic yeasts research in Indonesia.","authors":"Rika Indri Astuti, Muhammad Eka Prastya, Rahayu Wulan, Khairul Anam, Anja Meryandini","doi":"10.1093/femsyr/foad013","DOIUrl":"https://doi.org/10.1093/femsyr/foad013","url":null,"abstract":"Indonesia is a mega biodiversity country with various local wisdom, including the enormous variety of fermented foods and beverages. Indonesian researchers have conducted an intensive study to understand the diversity of microbes on those fermented products, one of which shows probiotic properties. Compared to that lactic acid bacteria, the study on probiotic yeasts is less explored. Probiotic yeast isolates are commonly isolated from traditional Indonesian fermented products. Saccharomyces, Pichia, and Candida are among Indonesia's most popular genera of probiotic yeasts, primarily applied in poultry and human health. The exploration of functional probiotic characteristics, such as antimicrobial, antifungal, antioxidant, and immunomodulator, has been widely reported from these local probiotic yeast strains. In vivo studies in a model organism such as mice conclude the prospective functional probiotic characteristics of the yeast isolates. Employment of current technology, such as omics, is essential in elucidating those functional properties. Advanced research and development of probiotic yeasts in Indonesia are gaining significant attention currently. For instance, probiotic yeasts-mediated fermentation in the production of kefir and kombucha are among the trend with promising economic value. The future trends of probiotic yeasts research in Indonesia are discussed in this review to give valuable sight into the application of indigenous probiotic yeasts in various fields.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"23 ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9474110","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: 1

Application of the fission yeast Schizosaccharomyces pombe in human nutrition. 裂糖酵母在人体营养中的应用。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2023-01-04 DOI: 10.1093/femsyr/foac064

Ee Sin Chen

引用次数: 1