Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increasing the efficiency of recombination-mediated genetic targeting. Here, we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step PCR-based and fusion PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomic assays at multipopulation and multispecies levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.
{"title":"GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems.","authors":"Zepu Miao, Haiting Wang, Xinyu Tu, Zhengshen Huang, Shujing Huang, Xinxin Zhang, Fan Wang, Zhishen Huang, Huihui Li, Yue Jiao, Song Gao, Zhipeng Zhou, Chun-Min Shan, Jing Li, Jia-Xing Yue","doi":"10.1002/yea.3916","DOIUrl":"10.1002/yea.3916","url":null,"abstract":"<p><p>Genetic targeting (e.g., gene knockout and tagging) based on polymerase chain reaction (PCR) is a simple yet powerful approach for studying gene functions. Although originally developed in classic budding and fission yeast models, the same principle applies to other eukaryotic systems with efficient homologous recombination. One-step PCR-based genetic targeting is conventionally used but the sizes of the homologous arms that it generates for recombination-mediated genetic targeting are usually limited. Alternatively, gene targeting can also be performed via fusion PCR, which can create homologous arms that are orders of magnitude larger, therefore substantially increasing the efficiency of recombination-mediated genetic targeting. Here, we present GetPrimers (https://www.evomicslab.org/app/getprimers/), a generalized computational framework and web tool to assist automatic targeting and verification primer design for both one-step PCR-based and fusion PCR-based genetic targeting experiments. Moreover, GetPrimers by design runs for any given genetic background of any species with full genome scalability. Therefore, GetPrimers is capable of empowering high-throughput functional genomic assays at multipopulation and multispecies levels. Comprehensive experimental validations have been performed for targeting and verification primers designed by GetPrimers across multiple organism systems and experimental setups. We anticipate GetPrimers to become a highly useful and popular tool to facilitate easy and standardized gene modification across multiple systems.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"19-34"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138471021","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}
Pub Date : 2024-01-01Epub Date: 2023-12-06DOI: 10.1002/yea.3913
Porfirio Gallegos-Casillas, Luis F García-Ortega, Adriana Espinosa-Cantú, J Abraham Avelar-Rivas, Carolina G Torres-Lagunes, Adrián Cano-Ricardez, Ángela M García-Acero, Susana Ruiz-Castro, Mayra Flores-Barraza, Alejandra Castillo, Fernando González-Zozaya, América Delgado-Lemus, Francisco Molina-Freaner, Cuauhtémoc Jacques-Hernández, Antonio Hernández-López, Luis Delaye, Xitlali Aguirre-Dugua, Manuel R Kirchmayr, Lucia Morales, Eugenio Mancera, Alexander DeLuna
Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX-1.0 culture collection by isolating 4524 strains from 68 sites with diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and validated a subset of the strains by ITS and D1/D2 sequencing, which also revealed two potential novel species of Saccharomycetales. Overall, the composition of yeast communities was weakly associated with local variables and types of climate, yet a core set of six species was consistently isolated from most producing regions. To explore the intraspecific variation of the yeasts from agave fermentations, we sequenced the genomes of four isolates of the nonconventional yeast Kazachstania humilis. The genomes of these four strains were substantially distinct from a European isolate of the same species, suggesting that they may belong to different populations. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments.
{"title":"Yeast diversity in open agave fermentations across Mexico.","authors":"Porfirio Gallegos-Casillas, Luis F García-Ortega, Adriana Espinosa-Cantú, J Abraham Avelar-Rivas, Carolina G Torres-Lagunes, Adrián Cano-Ricardez, Ángela M García-Acero, Susana Ruiz-Castro, Mayra Flores-Barraza, Alejandra Castillo, Fernando González-Zozaya, América Delgado-Lemus, Francisco Molina-Freaner, Cuauhtémoc Jacques-Hernández, Antonio Hernández-López, Luis Delaye, Xitlali Aguirre-Dugua, Manuel R Kirchmayr, Lucia Morales, Eugenio Mancera, Alexander DeLuna","doi":"10.1002/yea.3913","DOIUrl":"10.1002/yea.3913","url":null,"abstract":"<p><p>Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX-1.0 culture collection by isolating 4524 strains from 68 sites with diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and validated a subset of the strains by ITS and D1/D2 sequencing, which also revealed two potential novel species of Saccharomycetales. Overall, the composition of yeast communities was weakly associated with local variables and types of climate, yet a core set of six species was consistently isolated from most producing regions. To explore the intraspecific variation of the yeasts from agave fermentations, we sequenced the genomes of four isolates of the nonconventional yeast Kazachstania humilis. The genomes of these four strains were substantially distinct from a European isolate of the same species, suggesting that they may belong to different populations. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"35-51"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138488581","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}
Pub Date : 2024-01-01Epub Date: 2023-12-26DOI: 10.1002/yea.3920
Macarena Araya, Pablo Villarreal, Tomás Moyano, Ana R O Santos, Francisca P Díaz, Andrea Bustos-Jarufe, Kamila Urbina, Javier E Del Pino, Marizeth Groenewald, Rodrigo A Gutiérrez, Carlos A Rosa, Francisco A Cubillos
In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-BT revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375T . The Mycobank number is MB 849680.
在本研究中,我们描述了从智利阿塔卡马沙漠(Atacama Desert)的Neltuma chilensis植物样本中获得的新物种Nakazawaea atacamensis f. a., sp.从独立的 N. chilensis 样本(异名 Prosopis chilensis, Algarrobo)中总共获得了三株 N. atacamensis。其中两株是从树皮样本中获得的,第三株是从另一棵树的树皮渗出的树胶中获得的。利用分子特征对这一新物种进行了定义,并对其形态、生理和生化特性进行了鉴定。利用大亚基核糖体 RNA 基因 D1/D2 域序列进行的邻接分析表明,N. atacamensis 与 Nakazawaea pomicola 聚类。在 D1/D2 结构域中,N. atacamensis 与近缘种的序列相差 1.3%-5.2%。基于单核苷酸多态性数据的系统发生组分析证实,该新物种属于 Nakazawaea 属,其中 N. atacamensis 与 N. peltata 聚类。表型比较表明,与相关物种相比,N. atacamensis 表现出独特的碳同化模式。菌株 ATA-11A-BT 的基因组测序显示,其基因组大小约为 12.4 Mbp,与其他 Nakazawaea 物种相似,使用 InterProScan 对 5116 个蛋白编码基因进行了注释。此外,N. atacamensis 还具有发酵合成葡萄酒汁的能力,是一种潜在的用于单培养或共培养葡萄酒发酵的新酵母。这项全面的研究拓展了我们对 Nakazawaea 属的了解,并强调了 N. atacamensis 在发酵过程中的生态和工业潜力。N. atacamensis sp.Mycobank 编号为 MB 849680。
{"title":"Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert.","authors":"Macarena Araya, Pablo Villarreal, Tomás Moyano, Ana R O Santos, Francisca P Díaz, Andrea Bustos-Jarufe, Kamila Urbina, Javier E Del Pino, Marizeth Groenewald, Rodrigo A Gutiérrez, Carlos A Rosa, Francisco A Cubillos","doi":"10.1002/yea.3920","DOIUrl":"10.1002/yea.3920","url":null,"abstract":"<p><p>In this study, we describe Nakazawaea atacamensis f. a., sp. nov., a novel species obtained from Neltuma chilensis plant samples in Chile's hyperarid Atacama Desert. In total, three strains of N. atacamensis were obtained from independent N. chilensis samples (synonym Prosopis chilensis, Algarrobo). Two strains were obtained from bark samples, while the third strain was obtained from bark-exuded gum from another tree. The novel species was defined using molecular characteristics and subsequently characterized with respect to morphological, physiological, and biochemical properties. A neighbor-joining analysis using the sequences of the D1/D2 domains of the large subunit ribosomal RNA gene revealed that N. atacamensis clustered with Nakazawaea pomicola. The sequence of N. atacamensis differed from closely related species by 1.3%-5.2% in the D1/D2 domains. A phylogenomic analysis based on single-nucleotide polymorphism's data confirms that the novel species belongs to the genus Nakazawaea, where N. atacamensis clustered with N. peltata. Phenotypic comparisons demonstrated that N. atacamensis exhibited distinct carbon assimilation patterns compared to its related species. Genome sequencing of the strain ATA-11A-B<sup>T</sup> revealed a genome size of approximately 12.4 Mbp, similar to other Nakazawaea species, with 5116 protein-coding genes annotated using InterProScan. In addition, N. atacamensis exhibited the capacity to ferment synthetic wine must, representing a potential new yeast for mono or co-culture wine fermentations. This comprehensive study expands our understanding of the genus Nakazawaea and highlights the ecological and industrial potential of N. atacamensis in fermentation processes. The holotype of N. atacamensis sp. nov. is CBS 18375<sup>T</sup> . The Mycobank number is MB 849680.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"52-63"},"PeriodicalIF":2.2,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139037981","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}
Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C-terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co-transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD-less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re-establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.
{"title":"Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription?","authors":"Carlo Yague-Sanz","doi":"10.1002/yea.3921","DOIUrl":"https://doi.org/10.1002/yea.3921","url":null,"abstract":"Eukaryotic genes must be condensed into chromatin while remaining accessible to the transcriptional machinery to support gene expression. Among the three eukaryotic RNA polymerases (RNAP), RNAPII is unique, partly because of the C-terminal domain (CTD) of its largest subunit, Rpb1. Rpb1 CTD can be extensively modified during the transcription cycle, allowing for the co-transcriptional recruitment of specific interacting proteins. These include chromatin remodeling factors that control the opening or closing of chromatin. How the CTD-less RNAPI and RNAPIII deal with chromatin at rRNA and tRNA genes is less understood. Here, we review recent advances in our understanding of how the chromatin at tRNA genes and rRNA genes can be remodeled in response to environmental cues in yeast, with a particular focus on the role of local RNAPII transcription in recruiting chromatin remodelers at these loci. In fission yeast, RNAPII transcription at tRNA genes is important to re-establish a chromatin environment permissive to tRNA transcription, which supports growth from stationary phase. In contrast, local RNAPII transcription at rRNA genes correlates with the closing of the chromatin in starvation in budding and fission yeast, suggesting a role in establishing silent chromatin. These opposite roles might support a general model where RNAPII transcription recruits chromatin remodelers to tRNA and rRNA genes to promote the closing and reopening of chromatin in response to the environment.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"7 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138824838","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}
Daniel García-Ruano, Ian Hsu, Baptiste Leray, Bénédicte Billard, Gianni Liti, Damien Coudreuse
In poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates of Schizosaccharomyces pombe are homothallic. This allows them to naturally switch between the two h− and h+ mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of natural S. pombe isolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency.
在贫氮条件下,裂殖酵母细胞进行交配、减数分裂并形成孢子,从而抵御有害环境。裂殖酵母的天然分离物是同性的。这使它们能够高频率地在两种 h- 和 h+ 交配类型之间自然切换,从而确保细胞群体中同时存在两种交配伴侣。然而,改变交配型基因座可以取消交配型切换或将其降低到非常低的频率。这种异雄性菌株已被分离出来,并因其在孟德尔遗传学中的简单应用而成为研究实验室中的常见菌株。除了标准的实验室菌株外,现在还有大量的天然 S. pombe 分离物,它们是研究裂殖酵母遗传多样性和生物学的强大资源。然而,这些菌株大多是同雄性的,要从同雄性亲本中获得异雄性细胞,只能采用繁琐或诱变的策略。在这里,我们描述了一种生成异雄性菌株的简单方法。该方法利用了之前在交配型切换缺陷菌株中发现的交配型基因座的改变以及CRISPR-Cas9编辑工具,从而实现了一步到位的高效异雄性细胞工程。
{"title":"Engineering heterothallic strains in fission yeast","authors":"Daniel García-Ruano, Ian Hsu, Baptiste Leray, Bénédicte Billard, Gianni Liti, Damien Coudreuse","doi":"10.1002/yea.3914","DOIUrl":"https://doi.org/10.1002/yea.3914","url":null,"abstract":"In poor nitrogen conditions, fission yeast cells mate, undergo meiosis and form spores that are resistant to deleterious environments. Natural isolates of <i>Schizosaccharomyces pombe</i> are homothallic. This allows them to naturally switch between the two <i>h−</i> and <i>h+</i> mating types with a high frequency, thereby ensuring the presence of both mating partners in a population of cells. However, alteration of the mating type locus can abolish mating type switching or reduce it to a very low frequency. Such heterothallic strains have been isolated and are common in research laboratories due to the simplicity of their use for Mendelian genetics. In addition to the standard laboratory strains, a large collection of natural <i>S. pombe</i> isolates is now available, representing a powerful resource for investigating the genetic diversity and biology of fission yeast. However, most of these strains are homothallic, and only tedious or mutagenic strategies have been described to obtain heterothallic cells from a homothallic parent. Here, we describe a simple approach to generate heterothallic strains. It takes advantage of an alteration of the mating type locus that was previously identified in a mating type switching-deficient strain and the CRISPR-Cas9 editing tool, allowing for a one-step engineering of heterothallic cells with high efficiency.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"10 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138687440","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}
While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.
{"title":"Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation","authors":"Radityo Pangestu, Prihardi Kahar, Chiaki Ogino, Akihiko Kondo","doi":"10.1002/yea.3917","DOIUrl":"https://doi.org/10.1002/yea.3917","url":null,"abstract":"While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating <i>Saccharomyces cerevisiae</i> strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":"55 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138630574","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}
Pub Date : 2023-12-01Epub Date: 2023-10-26DOI: 10.1002/yea.3904
Neža Čadež, Kyria Boundy-Mills, Alfred Botha, Aleksey Kachalkin, Dénes Dlauchy, Gábor Péter
During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68-643T , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471T , MycoBank no.: 850126) are provided.
{"title":"Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species.","authors":"Neža Čadež, Kyria Boundy-Mills, Alfred Botha, Aleksey Kachalkin, Dénes Dlauchy, Gábor Péter","doi":"10.1002/yea.3904","DOIUrl":"10.1002/yea.3904","url":null,"abstract":"<p><p>During the course of independent studies in Europe, North America, and Africa, seven yeast strains were isolated from insect frass, decaying wood, tree flux, and olive oil sediment. Phylogenetic analysis of two barcoding DNA regions (internal transcribed spacer and the D1/D2 domain of the LSU rRNA gene) revealed that they belong to two closely related undescribed species distinct from all genera in the family Debaryomycetaceae. For reliable taxonomic placement the genomes of four strains of the two novel species and six type strains of closely related species were sequenced. Orthologous genes from 54 genomes of representatives of the Pichiomycetes and 23 outgroup taxa were concatenated to construct a fully supported phylogenetic tree. Consistent with the assumptions, we found that the two new species belong to a novel genus. In addition, the delimitation of the novel species was supported by genetic distance calculations from average nucleotide identity (ANI) and digital DNA:DNA hybridization (dDDH) values. The physiological characterization of the novel species was generally consistent with their genomic content. All strains had two alleles encoding secretory lipase in either two or three copies depending on the species. However, lipolytic activity was detected only in strains with three copies of the secretory lipase gene. Nevertheless, lipolytic activity might be related to their association with the insect gut. Based on these results, formal descriptions of the new genus Rasporella gen. nov. and of two new species Rasporella dianae sp. nov. (holotype UCDFST 68-643<sup>T</sup> , MycoBank no.: 850238) and Rasporella oleae sp. nov. (holotype ZIM 2471<sup>T</sup> , MycoBank no.: 850126) are provided.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"594-607"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54231274","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}
Pub Date : 2023-12-01Epub Date: 2023-11-23DOI: 10.1002/yea.3909
Evelyn Vásquez Castro, Golnaz Memari, Özge Ata, Diethard Mattanovich
Microbial metabolism offers a wide variety of opportunities to produce chemicals from renewable resources. Employing such processes of industrial biotechnology provides valuable means to fight climate change by replacing fossil feedstocks by renewable substrate to reduce or even revert carbon emission. Several yeast species are well suited chassis organisms for this purpose, illustrated by the fact that the still largest microbial production of a chemical, namely bioethanol is based on yeast. Although production of ethanol and some other chemicals is highly efficient, this is not the case for many desired bulk chemicals. One reason for low efficiency is carbon loss, which decreases the product yield and increases the share of total production costs that is taken by substrate costs. Here we discuss the causes for carbon loss in metabolic processes, approaches to avoid carbon loss, as well as opportunities to incorporate carbon from CO2 , based on the electron balance of pathways. These aspects of carbon efficiency are illustrated for the production of succinic acid from a diversity of substrates using different pathways.
{"title":"Carbon efficient production of chemicals with yeasts.","authors":"Evelyn Vásquez Castro, Golnaz Memari, Özge Ata, Diethard Mattanovich","doi":"10.1002/yea.3909","DOIUrl":"10.1002/yea.3909","url":null,"abstract":"<p><p>Microbial metabolism offers a wide variety of opportunities to produce chemicals from renewable resources. Employing such processes of industrial biotechnology provides valuable means to fight climate change by replacing fossil feedstocks by renewable substrate to reduce or even revert carbon emission. Several yeast species are well suited chassis organisms for this purpose, illustrated by the fact that the still largest microbial production of a chemical, namely bioethanol is based on yeast. Although production of ethanol and some other chemicals is highly efficient, this is not the case for many desired bulk chemicals. One reason for low efficiency is carbon loss, which decreases the product yield and increases the share of total production costs that is taken by substrate costs. Here we discuss the causes for carbon loss in metabolic processes, approaches to avoid carbon loss, as well as opportunities to incorporate carbon from CO<sub>2</sub> , based on the electron balance of pathways. These aspects of carbon efficiency are illustrated for the production of succinic acid from a diversity of substrates using different pathways.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"583-593"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10946752/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300147","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}
Pub Date : 2023-12-01Epub Date: 2023-11-22DOI: 10.1002/yea.3908
Koppisetty Viswa Chaithanya, Himanshu Sinha
MKT1 is a pleiotropic stress response gene identified by several quantitative trait studies with MKT189G as a causal variant, contributing to growth advantage in multiple stress environments. MKT1 has been shown to regulate HO endonuclease posttranscriptionally via the Pbp1-Pab1 complex. RNA-binding protein Puf3 modulates a set of nuclear-encoded mitochondrial transcripts whose expression was found to be affected by MKT1 alleles. This study attempts to relate the MKT1 allele-derived growth advantage with the stability of Puf3 targets during stress and elucidate the roles of Pbp1 and Puf3 in this mechanism. Our results showed that the growth advantage of the MKT189G allele in cycloheximide and H2 O2 was PBP1-dependent, whereas in 4-nitroquinoline 1-oxide, the growth advantage was dependent on both PUF3 and PBP1. We compared the messenger RNA decay kinetics of a set of Puf3 targets in multiple stress environments to understand the allele-specific regulation by MKT1. In oxidative stress, the MKT189G allele modulated the differential expression of nuclear-encoded mitochondrial genes in a PBP1- and PUF3-dependent manner. Additionally, MKT189G stabilised Puf3 targets, namely, COX17, MRS1 and RDL2, in an allele and stress-specific manner. Our results showed that COX17, MRS1 and RDL2 had a stress-specific response in stress environments, with the MKT189G allele contributing to better growth; this response was both PBP1- and PUF3-dependent. Our results indicate that the common allele, MKT189G , regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain's better growth in stress environments.
{"title":"MKT1 alleles regulate stress responses through posttranscriptional modulation of Puf3 targets in budding yeast.","authors":"Koppisetty Viswa Chaithanya, Himanshu Sinha","doi":"10.1002/yea.3908","DOIUrl":"10.1002/yea.3908","url":null,"abstract":"<p><p>MKT1 is a pleiotropic stress response gene identified by several quantitative trait studies with MKT1<sup>89G</sup> as a causal variant, contributing to growth advantage in multiple stress environments. MKT1 has been shown to regulate HO endonuclease posttranscriptionally via the Pbp1-Pab1 complex. RNA-binding protein Puf3 modulates a set of nuclear-encoded mitochondrial transcripts whose expression was found to be affected by MKT1 alleles. This study attempts to relate the MKT1 allele-derived growth advantage with the stability of Puf3 targets during stress and elucidate the roles of Pbp1 and Puf3 in this mechanism. Our results showed that the growth advantage of the MKT1<sup>89G</sup> allele in cycloheximide and H<sub>2</sub> O<sub>2</sub> was PBP1-dependent, whereas in 4-nitroquinoline 1-oxide, the growth advantage was dependent on both PUF3 and PBP1. We compared the messenger RNA decay kinetics of a set of Puf3 targets in multiple stress environments to understand the allele-specific regulation by MKT1. In oxidative stress, the MKT1<sup>89G</sup> allele modulated the differential expression of nuclear-encoded mitochondrial genes in a PBP1- and PUF3-dependent manner. Additionally, MKT1<sup>89G</sup> stabilised Puf3 targets, namely, COX17, MRS1 and RDL2, in an allele and stress-specific manner. Our results showed that COX17, MRS1 and RDL2 had a stress-specific response in stress environments, with the MKT1<sup>89G</sup> allele contributing to better growth; this response was both PBP1- and PUF3-dependent. Our results indicate that the common allele, MKT1<sup>89G</sup> , regulates stress responses by differentially stabilising Puf3-target mitochondrial genes, which allows for the strain's better growth in stress environments.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"616-627"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138291941","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}
Pub Date : 2023-12-01Epub Date: 2023-11-23DOI: 10.1002/yea.3911
Luisa Vivian Schwarz, Fernanda Knaach Sandri, Fernando Scariot, Ana Paula Longaray Delamare, Maria Jose Valera, Francisco Carrau, Sergio Echeverrigaray
Yeasts have been widely used as a model to better understand cell cycle mechanisms and how nutritional and genetic factors can impact cell cycle progression. While nitrogen scarcity is well known to modulate cell cycle progression, the relevance of nitrogen excess for microorganisms has been overlooked. In our previous work, we observed an absence of proper entry into the quiescent state in Hanseniaspora vineae and identified a potential link between this behavior and nitrogen availability. Furthermore, the Hanseniaspora genus has gained attention due to a significant loss of genes associated with DNA repair and cell cycle. Thus, the aim of our study was to investigate the effects of varying nitrogen concentrations on H. vineae's cell cycle progression. Our findings demonstrated that nitrogen excess, regardless of the source, disrupts cell cycle progression and induces G2/M arrest in H. vineae after reaching the stationary phase. Additionally, we observed a viability decline in H. vineae cells in an ammonium-dependent manner, accompanied by increased production of reactive oxygen species, mitochondrial hyperpolarization, intracellular acidification, and DNA fragmentation. Overall, our study highlights the events of the cell cycle arrest in H. vineae induced by nitrogen excess and attempts to elucidate the possible mechanism triggering this absence of proper entry into the quiescent state.
{"title":"High nitrogen concentration causes G2/M arrest in Hanseniaspora vineae.","authors":"Luisa Vivian Schwarz, Fernanda Knaach Sandri, Fernando Scariot, Ana Paula Longaray Delamare, Maria Jose Valera, Francisco Carrau, Sergio Echeverrigaray","doi":"10.1002/yea.3911","DOIUrl":"10.1002/yea.3911","url":null,"abstract":"<p><p>Yeasts have been widely used as a model to better understand cell cycle mechanisms and how nutritional and genetic factors can impact cell cycle progression. While nitrogen scarcity is well known to modulate cell cycle progression, the relevance of nitrogen excess for microorganisms has been overlooked. In our previous work, we observed an absence of proper entry into the quiescent state in Hanseniaspora vineae and identified a potential link between this behavior and nitrogen availability. Furthermore, the Hanseniaspora genus has gained attention due to a significant loss of genes associated with DNA repair and cell cycle. Thus, the aim of our study was to investigate the effects of varying nitrogen concentrations on H. vineae's cell cycle progression. Our findings demonstrated that nitrogen excess, regardless of the source, disrupts cell cycle progression and induces G2/M arrest in H. vineae after reaching the stationary phase. Additionally, we observed a viability decline in H. vineae cells in an ammonium-dependent manner, accompanied by increased production of reactive oxygen species, mitochondrial hyperpolarization, intracellular acidification, and DNA fragmentation. Overall, our study highlights the events of the cell cycle arrest in H. vineae induced by nitrogen excess and attempts to elucidate the possible mechanism triggering this absence of proper entry into the quiescent state.</p>","PeriodicalId":23870,"journal":{"name":"Yeast","volume":" ","pages":"640-650"},"PeriodicalIF":2.2,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138300149","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}