首页 > 最新文献

Yeast最新文献

英文 中文
GetPrimers: A generalized PCR-based genetic targeting primer designer enabling easy and standardized targeted gene modification across multiple systems. GetPrimers:一个通用的基于pcr的基因靶向引物设计器,可以跨多个系统进行简单和标准化的靶向基因修饰。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2023-12-02 DOI: 10.1002/yea.3916
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

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.

基于聚合酶链反应(PCR)的基因靶向(如基因敲除和标记)是研究基因功能的一种简单而有力的方法。虽然最初是在经典的出芽和裂变酵母模型中发展起来的,但同样的原理也适用于其他具有高效同源重组的真核生物系统。基于一步聚合酶链反应的基因靶向通常被使用,但它产生的同源臂的大小通常是有限的重组介导的基因靶向。或者,基因靶向也可以通过融合PCR进行,它可以创建大几个数量级的同源臂,因此大大提高了重组介导的基因靶向的效率。在这里,我们提出了GetPrimers (https://www.evomicslab.org/app/getprimers/),这是一个通用的计算框架和web工具,用于协助自动靶向和验证引物设计,用于一步pcr和融合pcr的基因靶向实验。此外,GetPrimers设计运行任何给定的遗传背景的任何物种与全基因组可扩展性。因此,GetPrimers能够在多种群和多物种水平上进行高通量功能基因组分析。GetPrimers设计的靶向和验证引物已经在多个生物系统和实验设置中进行了全面的实验验证。我们期望GetPrimers成为一个非常有用和流行的工具,以促进跨多个系统的简单和标准化的基因修饰。
{"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}
引用次数: 0
Yeast diversity in open agave fermentations across Mexico. 墨西哥龙舌兰露天发酵中的酵母多样性。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2023-12-06 DOI: 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.

酵母是一种广泛用于生产发酵食品和饮料的多种真菌微生物。在墨西哥,人们使用开放式发酵法从龙舌兰植物中提取烈酒。尽管这种传统做法在全国各地都很普遍,但人们只从数量有限的蒸馏器中分离和研究过酵母菌。为了系统地描述龙舌兰露天发酵过程中酵母物种的多样性,我们从气候、地理和生物环境各异的 68 个地点分离出 4524 株酵母,从而建立了 YMX-1.0 培养物库。我们使用 MALDI-TOF 质谱进行了分类,并通过 ITS 和 D1/D2 测序验证了一部分菌株,同时还发现了两个潜在的酵母菌纲新物种。总体而言,酵母群落的组成与当地变量和气候类型的关系不大,但在大多数产区都能分离出六个核心物种。为了探索龙舌兰发酵过程中酵母菌的种内变异,我们对非传统酵母 Kazachstania humilis 的四个分离株进行了基因组测序。这四株酵母的基因组与同种酵母的欧洲分离株有很大不同,这表明它们可能属于不同的种群。我们的工作有助于了解和保护具有重要文化和经济意义的开放式发酵系统,为研究生活在自然环境和人类相关环境交界处的微生物的生物学和遗传多样性提供了宝贵的资源。
{"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}
引用次数: 0
Nakazawaea atacamensis f.a., sp. nov. a novel nonconventional fermentative ascomycetous yeast species from the Atacama Desert. Nakazawaea atacamensis f.a.,sp. nov.来自阿塔卡马沙漠的一种新的非常规发酵子囊酵母菌。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2024-01-01 Epub Date: 2023-12-26 DOI: 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}
引用次数: 0
Shaping the chromatin landscape at rRNA and tRNA genes, an emerging new role for RNA polymerase II transcription? 塑造 rRNA 和 tRNA 基因的染色质景观,RNA 聚合酶 II 转录的新角色?
IF 2.6 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-21 DOI: 10.1002/yea.3921
Carlo Yague-Sanz
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.
真核生物基因必须凝集到染色质中,同时转录机制仍可利用它来支持基因表达。在真核生物的三种 RNA 聚合酶(RNAP)中,RNAPII 是独一无二的,部分原因在于其最大亚基 Rpb1 的 C 端结构域(CTD)。在转录周期中,Rpb1 CTD 可被广泛修饰,从而在共转录过程中招募特定的相互作用蛋白。其中包括控制染色质开放或关闭的染色质重塑因子。人们对无 CTD 的 RNAPI 和 RNAPIII 如何处理 rRNA 和 tRNA 基因上的染色质了解较少。在此,我们回顾了我们对 tRNA 基因和 rRNA 基因的染色质如何重塑以响应酵母环境线索的理解的最新进展,尤其关注局部 RNAPII 转录在这些位点招募染色质重塑因子的作用。在裂殖酵母中,tRNA 基因上的 RNAPII 转录对于重建允许 tRNA 转录的染色质环境非常重要,这有助于从静止期开始的生长。与此相反,rRNA 基因上的局部 RNAPII 转录与芽殖酵母和裂殖酵母饥饿时染色质的关闭有关,这表明 RNAPII 在建立沉默染色质方面发挥作用。这些相反的作用可能支持一种普遍的模式,即 RNAPII 转录将染色质重塑者招募到 tRNA 和 rRNA 基因上,以促进染色质的关闭和重新开放,从而对环境做出反应。
{"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}
引用次数: 0
Engineering heterothallic strains in fission yeast 裂变酵母中的异型菌株工程
IF 2.6 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-15 DOI: 10.1002/yea.3914
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}
引用次数: 0
Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation 乳酸发酵中絮凝酵母和非絮凝酵母对细胞密度和化学压力的比较反应
IF 2.6 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-11 DOI: 10.1002/yea.3917
Radityo Pangestu, Prihardi Kahar, Chiaki Ogino, Akihiko Kondo
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.
虽然絮凝已经证明了其在增强酵母健壮性和乙醇生产方面的功效,但其在乳酸发酵中的潜在应用仍未得到充分的探索。我们的研究考察了絮凝和非絮凝酿酒酵母菌株在结合外源乳酸途径、跨越不同细胞密度和存在木质纤维素衍生副产物时的代谢动力学差异。比较基因表达谱显示,在较高的细胞密度下培养非絮凝菌株,与糖酵解、能量代谢和其他关键途径相关的基因大幅上调,导致发酵产物水平升高。同时,无论细胞密度如何,絮凝菌株都表现出维持高糖酵解活性的固有能力。此外,我们的研究显示,在化学胁迫下糖酵解活性显著降低,这可能归因于能量投资阶段ATP供应的减少。相反,在絮凝菌株中形成的絮凝体对培养基中存在的有毒化学物质具有保护作用,促进更稳定的乳酸生产水平。此外,两种菌株的不同絮凝特性可能归因于絮凝蛋白基因及其调控因子的核苷酸序列的差异。本研究揭示了絮凝提高酵母乳酸产量的潜力,为菌株改良的代谢机制和潜在的基因靶点提供了见解。
{"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}
引用次数: 0
Taxogenomic placement of Rasporella oleae and Rasporella dianae gen. and spp. nov., two insect associated yeast species. 两个昆虫相关酵母种——夹竹桃和二氏桃的分类基因组定位。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-01 Epub Date: 2023-10-26 DOI: 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.

在欧洲、北美和非洲的独立研究过程中,从昆虫粪便、腐烂的木材、树木流量和橄榄油沉积物中分离出7种酵母菌株。对两个条形码DNA区域(LSU rRNA基因的内部转录间隔区和D1/D2结构域)的系统发育分析表明,它们属于两个密切相关的未描述物种,不同于无核菌科的所有属。为了进行可靠的分类学定位,对两个新物种的四个菌株和密切相关物种的六个模式菌株的基因组进行了测序。将来自Pichiomycetes代表性的54个基因组和23个外类群的同源基因连接起来,构建一个完全支持的系统发育树。与这些假设一致,我们发现这两个新物种属于一个新属。此外,根据平均核苷酸同一性(ANI)和数字DNA:DNA杂交(DDH)值进行的遗传距离计算支持了新物种的划界。新物种的生理特征与其基因组含量基本一致。所有菌株都有两个等位基因,编码分泌型脂肪酶,根据物种的不同,有两个或三个拷贝。然而,只有在具有三个分泌型脂肪酶基因拷贝的菌株中才检测到脂解活性。然而,脂解活性可能与它们与昆虫肠道的关系有关。基于这些结果,提供了新属Rasporella gen.nov.和两个新种Rasporella-dianae sp.nov.(正模UCDFST 68-643T,MycoBank编号:850238)和Rasporella-oleae sp.nov(正模ZIM 2471T,MycoBank编号:850126)的正式描述。
{"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}
引用次数: 0
Carbon efficient production of chemicals with yeasts. 利用酵母高效生产化学品。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-01 Epub Date: 2023-11-23 DOI: 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.

微生物代谢为从可再生资源生产化学物质提供了各种各样的机会。采用这种工业生物技术的过程提供了有价值的手段,以可再生基质取代化石原料,以减少甚至恢复碳排放,从而对抗气候变化。有几种酵母菌非常适合用于这一目的,这一事实表明,一种化学物质,即生物乙醇的最大微生物生产是基于酵母菌的。尽管乙醇和其他一些化学品的生产效率很高,但对于许多理想的散装化学品来说,情况并非如此。低效率的一个原因是碳损失,它降低了产品产量,增加了基材成本占总生产成本的份额。在这里,我们讨论了代谢过程中碳损失的原因,避免碳损失的方法,以及基于途径的电子平衡从CO2中吸收碳的机会。碳效率的这些方面说明了从使用不同途径的多种底物生产琥珀酸。
{"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}
引用次数: 0
MKT1 alleles regulate stress responses through posttranscriptional modulation of Puf3 targets in budding yeast. MKT1等位基因通过芽殖酵母Puf3靶点的转录后调控胁迫反应。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-01 Epub Date: 2023-11-22 DOI: 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.

MKT1是一个多效性的胁迫应答基因,在多个数量性状研究中被发现,MKT189G是一个因果变异,在多种胁迫环境下具有生长优势。MKT1已被证明通过Pbp1-Pab1复合物转录后调节HO内切酶。rna结合蛋白Puf3调节一组核编码的线粒体转录本,其表达被发现受MKT1等位基因的影响。本研究试图将MKT1等位基因衍生的生长优势与逆境中Puf3靶点的稳定性联系起来,并阐明Pbp1和Puf3在这一机制中的作用。结果表明,MKT189G等位基因在环己亚胺和H2 O2中的生长优势依赖于PBP1,而在4-硝基喹啉1-氧化物中的生长优势同时依赖于PUF3和PBP1。我们比较了一组Puf3靶点在多种应激环境下的信使RNA衰变动力学,以了解MKT1对等位基因的特异性调控。在氧化应激中,MKT189G等位基因以PBP1-和puf3依赖的方式调节核编码线粒体基因的差异表达。此外,MKT189G以等位基因和应激特异性的方式稳定Puf3靶点,即COX17、MRS1和rdr2。结果表明,COX17、MRS1和rdr2在逆境环境中具有特异性的应激反应,其中MKT189G等位基因有助于更好的生长;这种反应同时依赖于PBP1和puf3。我们的研究结果表明,共同等位基因MKT189G通过差异稳定puf3靶线粒体基因来调节应激反应,从而使菌株在应激环境中更好地生长。
{"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}
引用次数: 0
High nitrogen concentration causes G2/M arrest in Hanseniaspora vineae. 高氮浓度引起海参G2/M阻滞。
IF 2.2 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Pub Date : 2023-12-01 Epub Date: 2023-11-23 DOI: 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.

酵母已被广泛用作更好地理解细胞周期机制以及营养和遗传因素如何影响细胞周期进程的模型。众所周知,氮的缺乏可以调节细胞周期的进程,但氮过量与微生物的相关性一直被忽视。在我们之前的工作中,我们观察到在Hanseniaspora vineae中没有适当的进入静止状态,并确定了这种行为与氮可用性之间的潜在联系。此外,由于与DNA修复和细胞周期相关的基因显著缺失,Hanseniaspora属受到了关注。因此,我们的研究目的是探讨不同氮浓度对葡萄球菌细胞周期进程的影响。我们的研究结果表明,无论来源如何,过量的氮都会破坏细胞周期的进程,并在到达固定期后诱导葡萄球菌的G2/M停滞。此外,我们观察到H. vineae细胞的活力以氨依赖的方式下降,伴随着活性氧的增加、线粒体超极化、细胞内酸化和DNA断裂。总的来说,我们的研究强调了由氮过量诱导的葡萄球菌细胞周期停滞事件,并试图阐明引发这种缺乏适当进入静止状态的可能机制。
{"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}
引用次数: 0
期刊
Yeast
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1