Yeast最新文献 - Book学术

pSPObooster: A Plasmid System to Improve Sporulation Efficiency of Saccharomyces cerevisiae Lab Strains. pSPObooster：提高酿酒酵母实验室菌株繁殖效率的质粒系统

IF 2.2 4区生物学

Yeast Pub Date : 2024-10-01 Epub Date: 2024-09-09 DOI: 10.1002/yea.3978

Raphael Loll-Krippleber, Yangyang Kate Jiang, Grant W Brown

引用次数: 0

The 5-Fluorouracil RNA Expression Viewer (5-FU^R) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast. 5-氟尿嘧啶 RNA 表达查看器（5-FUR）有助于解读药物治疗和 RRP6 缺失对酵母转录景观的影响。

IF 2.2 4区生物学

Yeast Pub Date : 2024-10-01 Epub Date: 2024-09-30 DOI: 10.1002/yea.3982

Ugo Szachnowski, Oliver Sallou, Mateo Boudet, Anthony Bretaudeau, Maxime Wery, Antonin Morillon, Michael Primig

{"title":"The 5-Fluorouracil RNA Expression Viewer (5-FUR) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast.","authors":"Ugo Szachnowski, Oliver Sallou, Mateo Boudet, Anthony Bretaudeau, Maxime Wery, Antonin Morillon, Michael Primig","doi":"10.1002/yea.3982","DOIUrl":"10.1002/yea.3982","url":null,"abstract":"Saccharomyces cerevisiae is an excellent model to study the effect of external cues on cell division and stress response. 5-Fluorocuracil (5-FU) has been used to treat solid tumors since several decades. The drug was initially designed to interfere with DNA replication but was later found to exert its antiproliferative effect also via RNA-dependent processes. Since 5-FU inhibits the activity of the 3'-5'-exoribonuclease Rrp6 in yeast and mammals, earlier work has compared the effect of 5-FU treatment and RRP6 deletion at the transcriptome level in diploid synchronized yeast cells. To facilitate interpreting the expression data we have developed an improved 5-Fluorouracil RNA (5-FUR) expression viewer. Users can access information via genome coordinates and systematic or standard names for mRNAs and Xrn1-dependent-, stable-, cryptic-, and meiotic unannotated transcripts (XUTs, SUTs, CUTs, and MUTs). Normalized log2-transformed or linear data can be displayed as filled diagrams, line graphs or color-coded heatmaps. The expression data are useful for researchers interested in processes such as cell cycle regulation, mitotic repression of meiotic genes, the effect of 5-FU treatment and Rrp6 deficiency on the transcriptome and expression profiles of sense/antisense loci that encode overlapping transcripts. The viewer is accessible at http://5fur.genouest.org.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142355305","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

Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework. 通过生态本体框架探索酵母生态学

IF 2.6 4区生物学

Yeast Pub Date : 2024-09-18 DOI: 10.1002/yea.3981

Marie-Claire Harrison,Dana A Opulente,John F Wolters,Xing-Xing Shen,Xiaofan Zhou,Marizeth Groenewald,Chris Todd Hittinger,Antonis Rokas,Abigail Leavitt LaBella

{"title":"Exploring Saccharomycotina Yeast Ecology Through an Ecological Ontology Framework.","authors":"Marie-Claire Harrison,Dana A Opulente,John F Wolters,Xing-Xing Shen,Xiaofan Zhou,Marizeth Groenewald,Chris Todd Hittinger,Antonis Rokas,Abigail Leavitt LaBella","doi":"10.1002/yea.3981","DOIUrl":"https://doi.org/10.1002/yea.3981","url":null,"abstract":"Yeasts in the subphylum Saccharomycotina are found across the globe in disparate ecosystems. A major aim of yeast research is to understand the diversity and evolution of ecological traits, such as carbon metabolic breadth, insect association, and cactophily. This includes studying aspects of ecological traits like genetic architecture or association with other phenotypic traits. Genomic resources in the Saccharomycotina have grown rapidly. Ecological data, however, are still limited for many species, especially those only known from species descriptions where usually only a limited number of strains are studied. Moreover, ecological information is recorded in natural language format limiting high throughput computational analysis. To address these limitations, we developed an ontological framework for the analysis of yeast ecology. A total of 1,088 yeast strains were added to the Ontology of Yeast Environments (OYE) and analyzed in a machine-learning framework to connect genotype to ecology. This framework is flexible and can be extended to additional isolates, species, or environmental sequencing data. Widespread adoption of OYE would greatly aid the study of macroecology in the Saccharomycotina subphylum.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142257518","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

Improving an Alternative Glycerol Catabolism Pathway in Yarrowia lipolytica to Enhance Erythritol Production 改进脂肪分解酵母中的另一种甘油分解途径以提高赤藓糖醇产量

IF 2.6 4区生物学

Yeast Pub Date : 2024-09-12 DOI: 10.1002/yea.3980

Feng Liu, Jing‐Tao Tian, Ya‐Ting Wang, Lingxuan Zhao, Zhijie Liu, Jun Chen, Liu‐Jing Wei, Patrick Fickers, Qiang Hua

{"title":"Improving an Alternative Glycerol Catabolism Pathway in Yarrowia lipolytica to Enhance Erythritol Production","authors":"Feng Liu, Jing‐Tao Tian, Ya‐Ting Wang, Lingxuan Zhao, Zhijie Liu, Jun Chen, Liu‐Jing Wei, Patrick Fickers, Qiang Hua","doi":"10.1002/yea.3980","DOIUrl":"https://doi.org/10.1002/yea.3980","url":null,"abstract":"Engineering the glycerol‐3‐phosphate pathway could enhance erythritol production by accelerating glycerol uptake. However, little work has been conducted on the alternative dihydroxyacetone (DHA) pathway in Yarrowia lipolytica. Herein, this route was identified and characterized in Y. lipolytica by metabolomic and transcriptomic analysis. Moreover, the reaction catalyzed by dihydroxyacetone kinase encoded by dak2 was identified as the rate‐limiting step. By combining NHEJ‐mediated insertion mutagenesis with a push‐and‐pull strategy, Y. lipolytica strains with high‐yield erythritol synthesis from glycerol were obtained. Screening of a library of insertion mutants allows the identification of a mutant with fourfold increased erythritol production. Overexpression of DAK2 and glycerol dehydrogenase GCY3 together with gene encoding transketolase and transaldolase from the nonoxidative part of the pentose phosphate pathway led to a strain with further increased productivity with a titer of 53.1 g/L and a yield 0.56 g/g glycerol, which were 8.1‐ and 4.2‐fold of starting strain.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142226656","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

Rapid Fluorescence Assay for Polyphosphate in Yeast Extracts Using JC‐D7 利用 JC-D7 对酵母提取物中的多聚磷酸盐进行快速荧光测定

IF 2.6 4区生物学

Yeast Pub Date : 2024-09-12 DOI: 10.1002/yea.3979

Alexander Deitert, Jana Fees, Anna Mertens, Duc Nguyen Van, Maria Maares, Hajo Haase, Lars Mathias Blank, Claudia Keil

{"title":"Rapid Fluorescence Assay for Polyphosphate in Yeast Extracts Using JC‐D7","authors":"Alexander Deitert, Jana Fees, Anna Mertens, Duc Nguyen Van, Maria Maares, Hajo Haase, Lars Mathias Blank, Claudia Keil","doi":"10.1002/yea.3979","DOIUrl":"https://doi.org/10.1002/yea.3979","url":null,"abstract":"Polyphosphate (polyP) is an intriguing molecule that is found in almost any organism, covering a multitude of cellular functions. In industry, polyP is used due to its unique physiochemical properties, including pH buffering, water binding, and bacteriostatic activities. Despite the importance of polyP, its analytics is still challenging, with the gold standard being 31P NMR. Here, we present a simple staining method using the fluorescent dye JC‐D7 for the semi‐quantitative polyP evaluation in yeast extracts. Notably, fluorescence response was affected by polyP concentration and polymer chain length in the 0.5–500 µg/mL polyP concentration range. Hence, for polyP samples of unknown chain compositions, JC‐D7 cannot be used for absolute quantification. Fluorescence of JC‐D7 was unaffected by inorganic phosphate up to 50 mM. Trace elements (FeSO4 > CuSO4 > CoCl2 > ZnSO4) and toxic mineral salts (PbNO3 and HgCl2) diminished polyP–induced JC‐D7 fluorescence, affecting its applicability to samples containing polyP–metal complexes. The fluorescence was only marginally affected by other parameters, such as pH and temperature. After validation, this simple assay was used to elucidate the degree of polyP production by yeast strains carrying gene deletions in (poly)phosphate homeostasis. The results suggest that staining with JC‐D7 provides a robust and sensitive method for detecting polyP in yeast extracts and likely in extracts of other microbes. The simplicity of the assay enables high‐throughput screening of microbes to fully elucidate and potentially enhance biotechnological polyP production, ultimately contributing to a sustainable phosphorus utilization.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.6,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209970","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

In vitro activity of Western Australian honeys and Manuka honey against clinically important yeasts. 西澳大利亚蜂蜜和麦卢卡蜂蜜对临床重要酵母菌的体外活性。

IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-07-19 DOI: 10.1002/yea.3974

Robbie R Haines, Shuhui Xi, Kathryn J Green, Katherine A Hammer

{"title":"In vitro activity of Western Australian honeys and Manuka honey against clinically important yeasts.","authors":"Robbie R Haines, Shuhui Xi, Kathryn J Green, Katherine A Hammer","doi":"10.1002/yea.3974","DOIUrl":"10.1002/yea.3974","url":null,"abstract":"With the steady rise in antifungal resistance amongst clinically important yeasts, antifungal drug discovery remains of the utmost importance. To determine the potential of some honeys as alternative antifungal agents, we quantified the antifungal activity of 12 Western Australian honey samples, two Manuka honey samples and an artificial honey against 10 yeast isolates including clinical and reference strains. Results showed that the tested honeys varied in activity, and yeasts species also differed in susceptibility, with minimum inhibitory concentrations (MICs) determined by broth microdilution ranging from 8% to >44% w/v honey. Honeys with the highest overall activity were derived from Blackbutt (Eucalyptus patens), Jarrah (E. marginata), and Karri (E. diversicolor). The optical density of each MIC microtitre plate was determined after incubation and showed that at relatively low concentrations of honey the growth of all yeasts was enhanced compared to the untreated control, whereas at and above approximately 12% w/v, honeys exerted a dose-dependent growth inhibitory effect, the extent of which varied by honey type. Time-kill studies with 64% w/v honey showed that all eight of the natural honeys tested had greater fungicidal activity than the comparator artificial honey. Our findings suggest that the specific nectar-derived phytochemicals present within each honey play an important role in antifungal activity, and support the notion that activity is due to a combination of factors including osmotic activity, hydrogen peroxide and phytochemical compounds. These data indicate that honey is worthy of further investigation as a potential therapeutic agent for superficial yeast infections.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141731481","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

Using yeasts for the studies of nonfunctional factors in protein evolution. 利用酵母研究蛋白质进化中的非功能性因素。

IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-06-19 DOI: 10.1002/yea.3970

Katarzyna Potera, Katarzyna Tomala

{"title":"Using yeasts for the studies of nonfunctional factors in protein evolution.","authors":"Katarzyna Potera, Katarzyna Tomala","doi":"10.1002/yea.3970","DOIUrl":"10.1002/yea.3970","url":null,"abstract":"The evolution of protein sequence is driven not only by factors directly related to protein function and shape but also by nonfunctional factors. Such factors in protein evolution might be categorized as those connected to energetic costs, synthesis efficiency, and avoidance of misfolding and toxicity. A common approach to studying them is correlational analysis contrasting them with some characteristics of the protein, like amino acid composition, but these features are interdependent. To avoid possible bias, empirical studies are needed, and not enough work has been done to date. In this review, we describe the role of nonfunctional factors in protein evolution and present an experimental approach using yeast as a suitable model organism. The focus of the proposed approach is on the potential negative impact on the fitness of mutations that change protein properties not related to function and the frequency of mutations that change these properties. Experimental results of testing the misfolding avoidance hypothesis as an explanation for why highly expressed proteins evolve slowly are inconsistent with correlational research results. Therefore, more efforts should be made to empirically test the effects of nonfunctional factors in protein evolution and to contrast these results with the results of the correlational analysis approach.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421182","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

In vivo CRISPR-Cas9 expression in Candida glabrata, Candida bracarensis, and Candida nivariensis: A versatile tool to study chromosomal break repair. CRISPR-Cas9在格拉布氏念珠菌、布拉卡氏念珠菌和尼瓦瑞氏念珠菌中的体内表达：研究染色体断裂修复的多功能工具。

IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-08-09 DOI: 10.1002/yea.3976

Killian Métivier, Youfang Zhou-Li, Cécile Fairhead

引用次数: 0

Marker-free genomic editing in Saccharomyces cerevisiae using universal donor templates and multiplexing CRISPR-CAS9. 利用通用供体模板和复用 CRISPR-CAS9 在酿酒酵母中进行无标记基因组编辑。

IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-08-23 DOI: 10.1002/yea.3977

J H Grissom, S E Moody, R J Chi

{"title":"Marker-free genomic editing in Saccharomyces cerevisiae using universal donor templates and multiplexing CRISPR-CAS9.","authors":"J H Grissom, S E Moody, R J Chi","doi":"10.1002/yea.3977","DOIUrl":"10.1002/yea.3977","url":null,"abstract":"The budding yeast Saccharomyces cerevisiae is an excellent model organism for studying a variety of critical cellular processes. Traditional methods to knock in or -out at specific yeast loci utilize polymerase chain reaction-based techniques, in which marker cassettes with gene-specific homologies are integrated into the genome via homologous recombination. While simple and cost-effective, these methods are limited by marker availability when multiple edits are desired. More recently, CRISPR-Cas9 technology has introduced methods to edit the yeast genome without the need for selectable markers. Although efficient, this method is hindered by additional reagents and lengthy protocols to design and test unique guide RNAs and donor templates for each desired edit. In this study, we have combined these two approaches and have developed a highly efficient economical method to edit the yeast genome marker-free. We have designed two universal donor templates that efficiently repair commonly used selectable markers when targeted by a novel guideRNA-Cas9 designed to promoter regions in Ashbya gossypii found in most integration modules. Furthermore, we find our newly designed guideRNA-Cas9 successfully multiplexes when multiple markers are present. Using these new tools, we have significantly improved the cost and efficiency to generate single or multiple marker-free genetic modifications. In this study, we demonstrate the effectiveness of these new tools by marker-free ablating PRC1, PEP4, and PRB1 vacuolar proteases typically inactivated before many biochemical and membrane-trafficking studies using budding yeast.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047281","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

Synthetic lethality between toxic amino acids, RTG-target genes and chaperones in Saccharomyces cerevisiae. 有毒氨基酸、RTG 目标基因和伴侣蛋白在酿酒酵母中的合成致死率。

IF 2.2 4区生物学

Yeast Pub Date : 2024-09-01 Epub Date: 2024-07-30 DOI: 10.1002/yea.3975

Marina E Druseikis, Shay Covo

{"title":"Synthetic lethality between toxic amino acids, RTG-target genes and chaperones in Saccharomyces cerevisiae.","authors":"Marina E Druseikis, Shay Covo","doi":"10.1002/yea.3975","DOIUrl":"10.1002/yea.3975","url":null,"abstract":"The toxicity of non-proteinogenic amino acids has been known for decades. Numerous reports describe their antimicrobial/anticancer potential. However, these molecules are often toxic to the host as well; thus, a synthetic lethality approach that reduces the dose of these toxins while maintaining toxicity can be beneficial. Here we investigate synthetic lethality between toxic amino acids, the retrograde pathway, and molecular chaperones. In Saccharomyces cerevisiae, mitochondrial retrograde (RTG) pathway activation induces transcription of RTG-target genes to replenish alpha-ketoglutarate and its downstream product glutamate; both metabolites are required for arginine and lysine biosynthesis. We previously reported that tolerance of canavanine, a toxic arginine derivative, requires an intact RTG pathway, and low-dose canavanine exposure reduces the expression of RTG-target genes. Here we show that only a few of the examined chaperone mutants are sensitive to sublethal doses of canavanine. To predict synthetic lethality potential between RTG-target genes and chaperones, we measured the expression of RTG-target genes in canavanine-sensitive and canavanine-tolerant chaperone mutants. Most RTG-target genes were induced in all chaperone mutants starved for arginine; the same trend was not observed under lysine starvation. Canavanine exposure under arginine starvation attenuated and even reversed RTG-target-gene expression in the tested chaperone mutants. Importantly, under nearly all tested genetic and pharmacological conditions, the expression of IDH1 and/or IDH2 was induced. In agreement, idh1 and idh2 mutants are sensitive to canavanine and thialysine and show synthetic growth inhibition with chaperone mutants. Overall, we show that inhibiting molecular chaperones, RTG-target genes, or both can sensitize cells to low doses of toxic amino acids.","PeriodicalId":23870,"journal":{"name":"Yeast","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793596","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