FEMS yeast research最新文献_第7页

Using Euf1 transcription factor as a titrator of erythritol-inducible promoters in Yarrowia lipolytica; insight into the structure, splicing, and regulation mechanism. 利用 Euf1 转录因子作为脂肪溶解亚罗藻中赤藓糖醇诱导启动子的滴定剂；深入了解结构、剪接和调控机制。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae027

Ewelina Celińska, Paulina Korpys-Woźniak, Maria Gorczyca, Jean-Marc Nicaud

{"title":"Using Euf1 transcription factor as a titrator of erythritol-inducible promoters in Yarrowia lipolytica; insight into the structure, splicing, and regulation mechanism.","authors":"Ewelina Celińska, Paulina Korpys-Woźniak, Maria Gorczyca, Jean-Marc Nicaud","doi":"10.1093/femsyr/foae027","DOIUrl":"10.1093/femsyr/foae027","url":null,"abstract":"Controllable regulatory elements, like inducible, titratable promoters, are highly desired in synthetic biology toolboxes. A set of previously developed erythritol-inducible promoters along with an engineered Yarrowia lipolytica host strain were shown to be a very potent expression platform. In this study, we push the previously encountered limits of the synthetic promoters' titratability (by the number of upstream motifs) by using a compatible transcription factor, Euf1, as the promoter titrator. Overexpression of spliced EUF1 turned out to be very efficient in promoting expression from the compatible promoter, however, the erythritol-inducible character of the promoter was then lost. Analysis of the EUF1's splicing pattern suggests that the intron removal is promoted in the presence of erythritol, but is not dependent on it. The 3D structures of spliced versus unspliced Euf1 were modeled, and ligand-binding strength was calculated and compared. Furthermore, the EUF1-dependent expression profile under different chemical stimulants was investigated. Depletion of carbon source was identified as the significant factor upregulating the expression from the Euf1-dependent promoter (2-10-fold). Considering these findings and transcriptomics data, a new mechanism of the Euf1-regulated promoter action is proposed, involving a 'catabolite repression' transcription factor-Adr1, both acting on the same ERY-inducible promoter.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11394100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016873","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

Fermenting the future - on the benefits of a bioart collaboration. 发酵未来--生物艺术合作的益处。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae004

Diethard Mattanovich, Martin Altvater, Özge Ata, Simone Bachleitner

引用次数: 0

A novel fluorescence-activated cell sorting (FACS)-based screening identified ATG14, the gene required for pexophagy in the methylotrophic yeast. 一种基于荧光激活细胞分选（FACS）的新型筛选方法发现了ATG14，它是甲基营养酵母中进行pexophagy所需的基因。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae022

Kosuke Shiraishi, Yumi Arima, Motoharu Nakamura, Takumi Nakatsuji, Masahide Oku, Yasuyoshi Sakai

{"title":"A novel fluorescence-activated cell sorting (FACS)-based screening identified ATG14, the gene required for pexophagy in the methylotrophic yeast.","authors":"Kosuke Shiraishi, Yumi Arima, Motoharu Nakamura, Takumi Nakatsuji, Masahide Oku, Yasuyoshi Sakai","doi":"10.1093/femsyr/foae022","DOIUrl":"10.1093/femsyr/foae022","url":null,"abstract":"Pexophagy is a type of autophagy that selectively degrades peroxisomes and can be classified as either macropexophagy or micropexophagy. During macropexophagy, individual peroxisomes are sequestered by pexophagosomes and transported to the vacuole for degradation, while in micropexophagy, peroxisomes are directly engulfed by the septated vacuole. To date, some autophagy-related genes (ATGs) required for pexophagy have been identified through plate-based assays performed primarily under micropexophagy-induced conditions. Here, we developed a novel high-throughput screening system using fluorescence-activated cell sorting (FACS) to identify genes required for macropexophagy. Using this system, we discovered KpATG14, a gene that could not be identified previously in the methylotrophic yeast Komagataella phaffii due to technical limitations. Microscopic and immunoblot analyses found that KpAtg14 was required for both macropexophagy and micropexophagy. We also revealed that KpAtg14 was necessary for recruitment of the downstream factor KpAtg5 at the preautophagosomal structure (PAS), and consequently, for bulk autophagy. We anticipate our assay to be used to identify novel genes that are exclusively required for macropexophagy, leading to better understanding of the physiological significance of the existing two types of autophagic degradation pathways for peroxisomes.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11305268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141723350","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

Riboflavin overproduction on lignocellulose hydrolysate by the engineered yeast Candida famata. 工程酵母法氏念珠菌在木质纤维素水解物上过量产生核黄素。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae020

Ljubov S Dzanaeva, Dominik Wojdyła, Dariya V Fedorovych, Justyna Ruchala, Kostyantyn V Dmytruk, Andriy A Sibirny

{"title":"Riboflavin overproduction on lignocellulose hydrolysate by the engineered yeast Candida famata.","authors":"Ljubov S Dzanaeva, Dominik Wojdyła, Dariya V Fedorovych, Justyna Ruchala, Kostyantyn V Dmytruk, Andriy A Sibirny","doi":"10.1093/femsyr/foae020","DOIUrl":"10.1093/femsyr/foae020","url":null,"abstract":"Lignocellulose (dry plant biomass) is an abundant cheap inedible residue of agriculture and wood industry with great potential as a feedstock for biotechnological processes. Lignocellulosic substrates can serve as valuable resources in fermentation processes, allowing the production of a wide array of chemicals, fuels, and food additives. The main obstacle for cost-effective conversion of lignocellulosic hydrolysates to target products is poor metabolism of the major pentoses, xylose and L-arabinose, which are the second and third most abundant sugars of lignocellulose after glucose. We study the oversynthesis of riboflavin in the flavinogenic yeast Candida famata and found that all major lignocellulosic sugars, including xylose and L-arabinose, support robust growth and riboflavin synthesis in the available strains of C. famata. To further increase riboflavin production from xylose and lignocellulose hydrolysate, genes XYL1 and XYL2 coding for xylose reductase and xylitol dehydrogenase were overexpressed. The resulting strains exhibited increased riboflavin production in both shake flasks and bioreactors using diluted hydrolysate, reaching 1.5 g L-1.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11283204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141619785","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

Data integration strategies for whole-cell modeling. 全细胞建模的数据整合策略。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae011

Katja Tummler, Edda Klipp

引用次数: 0

Correction to: Yca1 metacaspase: diverse functions determine how yeast live and let die. 更正：Yca1元天冬酶：多种功能决定酵母如何生存和死亡

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae019

引用次数: 0

Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation. 在酿酒酵母中异源生产 pulcherrimin 可对肉毒菌分生孢子产生抑制作用。

IF 3.2 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foad053

Florian M Freimoser, Marina Mahler, Mark McCullough, Alexander O Brachmann, Lukas Nägeli, Maja Hilber-Bodmer, Jörn Piel, Stefan A Hoffmann, Yizhi Cai

{"title":"Heterologous pulcherrimin production in Saccharomyces cerevisiae confers inhibitory activity on Botrytis conidiation.","authors":"Florian M Freimoser, Marina Mahler, Mark McCullough, Alexander O Brachmann, Lukas Nägeli, Maja Hilber-Bodmer, Jörn Piel, Stefan A Hoffmann, Yizhi Cai","doi":"10.1093/femsyr/foad053","DOIUrl":"10.1093/femsyr/foad053","url":null,"abstract":"Pulcherrimin is an iron (III) chelate of pulcherriminic acid that plays a role in antagonistic microbial interactions, iron metabolism, and stress responses. Some bacteria and yeasts produce pulcherriminic acid, but so far, pulcherrimin could not be produced in Saccharomyces cerevisiae. Here, multiple integrations of the Metschnikowia pulcherrima PUL1 and PUL2 genes in the S. cerevisiae genome resulted in red colonies, which indicated pulcherrimin formation. The coloration correlated positively and significantly with the number of PUL1 and PUL2 genes. The presence of pulcherriminic acid was confirmed by mass spectrometry. In vitro competition assays with the plant pathogenic fungus Botrytis caroliana revealed inhibitory activity on conidiation by an engineered, strong pulcherrimin-producing S. cerevisiae strain. We demonstrate that the PUL1 and PUL2 genes from M. pulcherrima, in multiple copies, are sufficient to transfer pulcherrimin production to S. cerevisiae and represent the starting point for engineering and optimizing this biosynthetic pathway in the future.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10786192/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138884786","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

Sphingolipid diversity in Candida auris: unraveling interclade and drug resistance fingerprints. 白色念珠菌的鞘脂多样性：揭示支链间和耐药性指纹。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae008

Basharat Ali, Mohit Kumar, Praveen Kumar, Anshu Chauhan, Sana Akhtar Usmani, Shivaprakash M Rudramurthy, Jacques F Meis, Arunaloke Chakrabarti, Ashutosh Singh, Naseem A Gaur, Alok K Mondal, Rajendra Prasad

{"title":"Sphingolipid diversity in Candida auris: unraveling interclade and drug resistance fingerprints.","authors":"Basharat Ali, Mohit Kumar, Praveen Kumar, Anshu Chauhan, Sana Akhtar Usmani, Shivaprakash M Rudramurthy, Jacques F Meis, Arunaloke Chakrabarti, Ashutosh Singh, Naseem A Gaur, Alok K Mondal, Rajendra Prasad","doi":"10.1093/femsyr/foae008","DOIUrl":"10.1093/femsyr/foae008","url":null,"abstract":"In this study, we explored the sphingolipid (SL) landscape in Candida auris, which plays pivotal roles in fungal biology and drug susceptibility. The composition of SLs exhibited substantial variations at both the SL class and molecular species levels among clade isolates. Utilizing principal component analysis, we successfully differentiated the five clades based on their SL class composition. While phytoceramide (PCer) was uniformly the most abundant SL class in all the isolates, other classes showed significant variations. These variations were not limited to SL class level only as the proportion of different molecular species containing variable number of carbons in fatty acid chains also differed between the isolates. Also a comparative analysis revealed abundance of ceramides and glucosylceramides in fluconazole susceptible isolates. Furthermore, by comparing drug-resistant and susceptible isolates within clade IV, we uncovered significant intraclade differences in key SL classes such as high PCer and low long chain base (LCB) content in resistant strains, underscoring the impact of SL heterogeneity on drug resistance development in C. auris. These findings shed light on the multifaceted interplay between genomic diversity, SLs, and drug resistance in this emerging fungal pathogen.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941814/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140039069","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

Application of unimodal probability distribution models for morphological phenotyping of budding yeast. 单模态概率分布模型在芽殖酵母形态表型中的应用

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foad056

Yoshikazu Ohya, Farzan Ghanegolmohammadi, Kaori Itto-Nakama

{"title":"Application of unimodal probability distribution models for morphological phenotyping of budding yeast.","authors":"Yoshikazu Ohya, Farzan Ghanegolmohammadi, Kaori Itto-Nakama","doi":"10.1093/femsyr/foad056","DOIUrl":"10.1093/femsyr/foad056","url":null,"abstract":"Morphological phenotyping of the budding yeast Saccharomyces cerevisiae has helped to greatly clarify the functions of genes and increase our understanding of cellular functional networks. It is necessary to understand cell morphology and perform quantitative morphological analysis (QMA) but assigning precise values to morphological phenotypes has been challenging. We recently developed the Unimodal Morphological Data image analysis pipeline for this purpose. All true values can be estimated theoretically by applying an appropriate probability distribution if the distribution of experimental values follows a unimodal pattern. This reliable pipeline allows several downstream analyses, including detection of subtle morphological differences, selection of mutant strains with similar morphology, clustering based on morphology, and study of morphological diversity. In addition to basic research, morphological analyses of yeast cells can also be used in applied research to monitor breeding and fermentation processes and control the fermentation activity of yeast cells.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10804223/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139086547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring yeast biodiversity and process conditions for optimizing ethylene glycol conversion into glycolic acid. 探索酵母生物多样性和工艺条件，优化乙二醇转化为乙醇酸的过程。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2024-01-09 DOI: 10.1093/femsyr/foae024

Vittorio Giorgio Senatore, Riccardo Milanesi, Fiorella Masotti, Letizia Maestroni, Stefania Pagliari, Ciro Cannavacciuolo, Luca Campone, Immacolata Serra, Paola Branduardi

{"title":"Exploring yeast biodiversity and process conditions for optimizing ethylene glycol conversion into glycolic acid.","authors":"Vittorio Giorgio Senatore, Riccardo Milanesi, Fiorella Masotti, Letizia Maestroni, Stefania Pagliari, Ciro Cannavacciuolo, Luca Campone, Immacolata Serra, Paola Branduardi","doi":"10.1093/femsyr/foae024","DOIUrl":"10.1093/femsyr/foae024","url":null,"abstract":"Plastics have become an indispensable material in many fields of human activities, with production increasing every year; however, most of the plastic waste is still incinerated or landfilled, and only 10% of the new plastic is recycled even once. Among all plastics, polyethylene terephthalate (PET) is the most produced polyester worldwide; ethylene glycol (EG) is one of the two monomers released by the biorecycling of PET. While most research focuses on bacterial EG metabolism, this work reports the ability of Saccharomyces cerevisiae and nine other common laboratory yeast species not only to consume EG, but also to produce glycolic acid (GA) as the main by-product. A two-step bioconversion of EG to GA by S. cerevisiae was optimized by a design of experiment approach, obtaining 4.51 ± 0.12 g l-1 of GA with a conversion of 94.25 ± 1.74% from 6.21 ± 0.04 g l-1 EG. To improve the titer, screening of yeast biodiversity identified Scheffersomyces stipitis as the best GA producer, obtaining 23.79 ± 1.19 g l-1 of GA (yield 76.68%) in bioreactor fermentation, with a single-step bioprocess. Our findings contribute in laying the ground for EG upcycling strategies with yeasts.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141893228","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