FEMS yeast research最新文献_第9页

Comparison of stress tolerance mechanisms between Saccharomyces cerevisiae and the multistress-tolerant Pichia kudriavzevii. 酿酒酵母与多重抗逆性毕赤酵母的抗逆性机制比较。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf024

Thasneem Banu Frousnoon, Nam Ngoc Pham, Zong-Yen Wu, Ping-Hung Hsieh, Yasuo Yoshikuni

{"title":"Comparison of stress tolerance mechanisms between Saccharomyces cerevisiae and the multistress-tolerant Pichia kudriavzevii.","authors":"Thasneem Banu Frousnoon, Nam Ngoc Pham, Zong-Yen Wu, Ping-Hung Hsieh, Yasuo Yoshikuni","doi":"10.1093/femsyr/foaf024","DOIUrl":"10.1093/femsyr/foaf024","url":null,"abstract":"Yeasts play a vital role in both research and industrial biomanufacturing. Saccharomyces cerevisiae has been extensively utilized as a model system. However, its application is often constrained by limited tolerance to the diverse stress conditions encountered in bioprocesses. These challenges have driven increasing interest in nonconventional, multistress-tolerant yeasts as alternative biomanufacturing hosts. This review highlights Pichia kudriavzevii as a promising nonconventional yeast for industrial applications. Unlike S. cerevisiae, P. kudriavzevii exhibits exceptional tolerance to high temperatures, elevated concentrations of furanic and phenolic inhibitors, osmotic stress, salinity, and extreme pH. These traits make it an attractive candidate for industrial processes without requiring extensive genetic modifications to enhance stress resistance. As a result, P. kudriavzevii has emerged as a flagship species for advancing bioeconomy. Despite its industrial potential, the molecular mechanisms underlying P. kudriavzevii's superior stress tolerance remain poorly understood. This review compiles current knowledge on P. kudriavzevii and compares its stress tolerance mechanisms with those of S. cerevisiae, providing insights into its innate resilience. By expanding our understanding of nonconventional yeasts, this review aims to facilitate their broader adoption as robust microbial platforms for industrial biomanufacturing.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12097485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143994230","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

Taxogenomic analysis of Pichia senei sp. nov. and new insights into hybridization events in the Pichia cactophila species complex. 毕赤酵母（Pichia senei sp. 11 .）的分类基因组学分析及毕赤酵母种群杂交事件的新见解。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf037

Katharina O Barros, Jassim Al-Oboudi, Larissa F D Freitas, Francisca M P Sousa, Thiago M Batista, Ana Raquel O Santos, Paula B Morais, José Paulo Sampaio, Marc-André Lachance, Chris Todd Hittinger, Carlos A Rosa

{"title":"Taxogenomic analysis of Pichia senei sp. nov. and new insights into hybridization events in the Pichia cactophila species complex.","authors":"Katharina O Barros, Jassim Al-Oboudi, Larissa F D Freitas, Francisca M P Sousa, Thiago M Batista, Ana Raquel O Santos, Paula B Morais, José Paulo Sampaio, Marc-André Lachance, Chris Todd Hittinger, Carlos A Rosa","doi":"10.1093/femsyr/foaf037","DOIUrl":"10.1093/femsyr/foaf037","url":null,"abstract":"Three strains of a novel yeast species were isolated from necrotic cactus tissues of Cereus saddianus and Micranthocereus dolichospermaticus and from phytotelmata of Bromelia karatas. DNA sequence analysis of the Internal Transcribed Spacer (ITS) region and D1/D2 domains of the large subunit ribosomal RNA, along with whole genome phylogenomic analysis, showed that this yeast is most closely related to Pichia insulana, Pichia cactophila, and Pichia inconspicua. The new species differs by 10-13 nucleotide substitutions from these species in D1/D2 sequences and exhibits <90% genome-wide average nucleotide identity to them. The name Pichia senei sp. nov. is proposed for the novel species, which is homothallic and produces asci with one to four hat-shaped ascospores. The holotype is CBS 16311 (MycoBank MB 858723). Taxogenomic analyses of the P. cactophila species complex, including P. senei, provide new insights about the hybridizations events that shaped this group. Pichia insulana and P. inconspicua are identified as the parental lineages that originated P. cactophila, and P. senei also appears closely related to one of the progenitors of P. inconspicua. We assess phylogeny, heterozygosity, and ploidy to explore the processes shaping diversity, showing how genomic data support yeast species delimitation and reveal complex hybridization.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12359136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144834676","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

Harnessing yeasts for sustainable succinic acid production: advances in metabolic engineering and biorefinery integration. 利用酵母可持续生产琥珀酸：代谢工程和生物炼制一体化的进展。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf052

Vasiliki Korka, Apostolos Petropoulos, Sofia Maria Ioannidou, Carol Sze Ki Lin, Apostolis Koutinas, Patrick Fickers

{"title":"Harnessing yeasts for sustainable succinic acid production: advances in metabolic engineering and biorefinery integration.","authors":"Vasiliki Korka, Apostolos Petropoulos, Sofia Maria Ioannidou, Carol Sze Ki Lin, Apostolis Koutinas, Patrick Fickers","doi":"10.1093/femsyr/foaf052","DOIUrl":"10.1093/femsyr/foaf052","url":null,"abstract":"This review highlights the potential of Yarrowia lipolytica and other yeasts as sustainable producers of bio-based succinic acid (SA), a key platform chemical with applications in bioplastics, solvents, and pharmaceuticals. Recent advances in metabolic engineering have substantially improved SA titers, yields, and productivities in yeasts. These improvements were achieved by reconstructing biosynthetic pathways, disrupting gene involved in side-metabolism and/or expressing heterologous genes involved in critical metabolic functions. The use of renewable feedstocks, including crude glycerol, agricultural residues, food waste hydrolysates, and industrial by-products, has shown promise in reducing both production costs and environmental impacts. Innovative downstream separation techniques, such as in situ extraction, membrane filtration, and crystallization, further contribute to process sustainability. Integrating yeast-based SA production into circular biorefineries and adopting continuous production systems are promising strategies for enhancing economic feasibility and minimizing ecological footprints. Although challenges related to scale-up and process integration persist, ongoing advancements in genetic engineering and bioprocessing technologies position yeast-based processes as a viable route for sustainable, large-scale bio-based SA production within a circular bioeconomy framework.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12501425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091603","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

Yeast-secreted compounds with antifungal activity-screening, genetic parts, biosynthetic pathways, and regulation. 具有抗真菌活性的酵母菌分泌化合物-筛选，遗传部分，生物合成途径和调控。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf068

Alicia Maciá Valero, Min Lu, Sonja Billerbeck

{"title":"Yeast-secreted compounds with antifungal activity-screening, genetic parts, biosynthetic pathways, and regulation.","authors":"Alicia Maciá Valero, Min Lu, Sonja Billerbeck","doi":"10.1093/femsyr/foaf068","DOIUrl":"10.1093/femsyr/foaf068","url":null,"abstract":"Awareness is rising that antifungal resistance poses a threat to agriculture, food safety, biodiversity, and human health. There is a limited number of antifungals available and resistance to all of them has been reported. The development of novel antifungals is complex, as eukaryotic organisms have very few selective drug targets that distinguish them from the infected plant, human, or animal host. Yeasts produce different compounds with antifungal activity, ranging from small molecules such as iron chelators, biosurfactants, and volatile organic compounds, to proteins like myocins and hydrolytic enzymes. Those could be further developed into new antifungals; however, there is a scarcity of fundamental knowledge on their chemical structure, their mode of action, their biosynthesis, and its regulation. Given the opportunities that yeasts display as industrial hosts and the synthetic biology tools available, a deeper understanding of these molecular aspects could enable a wider range of yet underexplored applications for the producer yeast and their molecules, from biocontrol to food preservation and human health. To facilitate this exploration, we here consolidate current molecular knowledge on these compounds, suggest readily available methodologies to screen for different molecule classes in natural yeast isolates and discuss how they could be further studied and engineered towards their eventual application.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12715866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145548966","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 emerging roles of non-Saccharomyces yeasts in fermented foods and human health. 非酵母菌酵母在发酵食品和人类健康中的新作用。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf056

Alexandra Imre, Nathan Crook

引用次数: 0

Integrating yeast biodiversity and machine learning for predictive metabolic engineering. 酵母生物多样性与机器学习在预测代谢工程中的整合。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf072

Akaraphol Watcharawipas, Weerawat Runguphan, Peerapat Khamwachirapithak, Thanaporn Laothanachareon

{"title":"Integrating yeast biodiversity and machine learning for predictive metabolic engineering.","authors":"Akaraphol Watcharawipas, Weerawat Runguphan, Peerapat Khamwachirapithak, Thanaporn Laothanachareon","doi":"10.1093/femsyr/foaf072","DOIUrl":"10.1093/femsyr/foaf072","url":null,"abstract":"Yeast biodiversity and machine learning (ML) are transforming the landscape of metabolic engineering. While Saccharomyces cerevisiae remains foundational to industrial biotechnology due to its genetic tractability and robust growth, it struggles to synthesize complex metabolites, utilize alternative feedstocks, and withstand industrial stresses. Non-conventional yeasts such as Yarrowia lipolytica and Ogataea polymorpha possess traits such as thermotolerance, acid resistance, and lipid accumulation, making them promising alternatives. However, broader adoption remains limited by insufficient genetic tools and low predictability of engineered components across species. Recent ML advances are addressing these gaps by enabling accurate prediction of genetic part function, optimizing gene expression, and discovering novel biosynthetic components in diverse yeasts. These tools support rational selection of genetic elements and pathway configurations tailored to non-model hosts, streamlining the design-build-test-learn cycle. Leveraging biodiversity expands the available yeast chassis and toolkits, improving strain robustness under industrial conditions. This mini-review discusses how yeast biodiversity is being harnessed to broaden engineering strategies and highlights recent ML advances driving data-guided strain and pathway design. Special attention is given to ML-guided identification and optimization of genetic elements. Together, evolutionary diversity and intelligent computation promise more modular, predictive, and scalable yeast platforms for next-generation metabolic engineering.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12715865/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145667967","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. 携带改良甘油-3-磷酸和甘油利用合成二羟基丙酮途径的工程酿酒酵母菌株的生理特性。

IF 3.5 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":3.5,"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

Stress-induced ribosomal heterogeneity in Saccharomyces cerevisiae: from protein paralogs to regulatory noncoding RNAs. 应激诱导的酿酒酵母核糖体异质性：从蛋白质类似性到调节性非编码rna。

IF 2.7 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf050

Agata Tyczewska, Kamilla Bąkowska-Żywicka

{"title":"Stress-induced ribosomal heterogeneity in Saccharomyces cerevisiae: from protein paralogs to regulatory noncoding RNAs.","authors":"Agata Tyczewska, Kamilla Bąkowska-Żywicka","doi":"10.1093/femsyr/foaf050","DOIUrl":"10.1093/femsyr/foaf050","url":null,"abstract":"Ribosomes, once considered uniform protein biosynthesis machines, are now recognized as heterogeneous and dynamic entities with specialized functions. In Saccharomyces cerevisiae, ribosomal heterogeneity arises from variability in ribosomal protein (RP) composition, rRNA sequence polymorphisms, post-transcriptional modifications, and associations with ribosome-associated factors and noncoding RNAs. RP gene (RPG) paralogs and their differential expression influence growth, stress resistance, and drug responses. Introns and untranslated regions in RPGs regulate expression under stress, while ribosome composition adjusts to environmental cues via altered RP stoichiometry and post-translational modifications, such as phosphorylation and ubiquitination. Additionally, ribosome-associated factors contribute to selective translation of specific mRNA subsets. Ribosomal RNA heterogeneity, though less studied in yeast, is evident through polymorphisms in rDNA arrays and post-transcriptional modifications like pseudouridylation and 2'-O-ribose methylation. Furthermore, transient associations with small noncoding RNAs (e.g. tRNA-, snoRNA-, and mRNA-derived fragments) modulate translation in a stress-dependent manner, supporting the concept of specialized ribosomes. Despite growing evidence, functional significance of ribosome specialization remains under debate. Future research aims to uncover the extent, regulation, and biological roles of ribosome heterogeneity across organisms and conditions. Emerging tools such as ribosome sequencing, single-molecule fluorescence resonance energy transfer, and single-molecule fluorescence resonance energy transfer offer promising avenues to resolve these questions and reveal how specialized ribosomes contribute to adaptive gene expression.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":"25 ","pages":""},"PeriodicalIF":2.7,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12461147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136792","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

Lignocellulosic biomass fermentation: a roadmap for Candida famata and Ogataea polymorpha. 木质纤维素生物质发酵：假丝酵母和多形Ogataea的路线图。

IF 3.5 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf046

Dominik Wojdyła, Roksolana Vasylyshyn, Alicja Najdecka, Justyna Ruchala

引用次数: 0