FEMS yeast research最新文献_第4页

Assessing methods for estimating microbial lag phase duration: a comparative analysis using Saccharomyces cerevisiae empirical and simulated data. 估算微生物滞后期的评估方法：利用酿酒酵母的经验和模拟数据进行比较分析。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf033

Monika Opalek, Dominika Wloch-Salamon, Bogna J Smug

{"title":"Assessing methods for estimating microbial lag phase duration: a comparative analysis using Saccharomyces cerevisiae empirical and simulated data.","authors":"Monika Opalek, Dominika Wloch-Salamon, Bogna J Smug","doi":"10.1093/femsyr/foaf033","DOIUrl":"10.1093/femsyr/foaf033","url":null,"abstract":"The lag phase is a temporary, nonreplicative period observed when a microbial population is introduced to a new, nutrient-rich environment. Although the theoretical concept of growth phases is clear, the practical application of methods for estimating lag lengths is often challenging. In fact, there are two distinct assumptions: (i) that cells do not divide at all during the lag phase or (ii) that they divide but at a suboptimal rate. Therefore, the choice of method should consider not only technical limitations but also consistency with the biological context. Here, we investigate the performance of the most common lag estimation methods, using empirical and simulated datasets. We apply different biological scenarios and simulate curves with varying parameters (i.e. growth rate, noise level, and frequency of measurements) to test their impact on the estimated lag phase duration. Our validation shows that infrequent measurements, low growth rate, longer lag phases, or higher level of noise in the measurements result in higher bias and higher variance of lag estimation. Additionally, in case of noisy data, the methods relying on model fitting perform best.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12258147/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144607893","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

Linking endo-lysosomal pH, sterol, and trafficking to neurodegenerative disease. 内溶酶体pH值、固醇和转运与神经退行性疾病的关系。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf034

Hari Prasad, Rajini Rao

{"title":"Linking endo-lysosomal pH, sterol, and trafficking to neurodegenerative disease.","authors":"Hari Prasad, Rajini Rao","doi":"10.1093/femsyr/foaf034","DOIUrl":"10.1093/femsyr/foaf034","url":null,"abstract":"Although endo-lysosomal abnormalities have been recognized as a pathognomonic feature of Alzheimer's disease, the lack of druggable targets has hampered the translation from bench to bedside. This article provides an overview of the insights gained from yeast research with a focus on understudied luminal acidification mechanisms and their major impact on disease progression. The yeast-to-human discovery and validation strategy identified a \"druggable\" triad featuring luminal pH, sterol content, and trafficking that (dys)regulate reciprocally. Endosomal Na+/H+ exchangers (eNHE), discovered in yeast and later described in mammals, provide independent support for this pathogenic model. The brain is often the most severely affected organ in patients with eNHE mutations, and a subset is causally linked to progressive and severe neurodegeneration, demonstrating that neurons heavily rely on fine-tuning of endosomal pH. We present recent advances on the role of eNHE in ageing related neurodegenerative diseases, which has implications for pathogenesis and therapy. Future studies should unravel the broader landscape of endo-lysosomal pH in neurodegenerative diseases. Given that pharmacologic correction of luminal hyperacidification defect completely ameliorates endo-lysosomal deficits in eNHE deletion yeast, there is compelling reason to believe that efforts to target endo-lysosomal acid-base homeostasis will eventually lead to novel therapeutic approaches for neurodegenerative diseases.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12268332/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144590797","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

Recent progress in engineering yeast producers of cellulosic ethanol. 纤维素乙醇工程酵母生产研究进展。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf035

Roksolana Vasylyshyn, Justyna Ruchala, Kostyantyn Dmytruk, Andriy Sibirny

{"title":"Recent progress in engineering yeast producers of cellulosic ethanol.","authors":"Roksolana Vasylyshyn, Justyna Ruchala, Kostyantyn Dmytruk, Andriy Sibirny","doi":"10.1093/femsyr/foaf035","DOIUrl":"10.1093/femsyr/foaf035","url":null,"abstract":"The production of second-generation (2 G) bioethanol, a key sector in industrial biotechnology, addresses the demand for sustainable energy by utilizing lignocellulosic biomass. Efficient fermentation of all sugars from lignocellulose hydrolysis is essential to enhance ethanol titers, improve biomass-to-biofuel yields, and lower costs. This review compares the potential of recombinant yeast strains for 2 G bioethanol production, focusing on their ability to metabolize diverse sugars, particularly xylose. Saccharomyces cerevisiae, engineered for enhanced pentose and hexose utilization, is compared with the nonconventional yeasts Scheffersomyces stipitis, Kluyveromyces marxianus, and Ogataea polymorpha. Key factors include sugar assimilation pathways, cofermentation with glucose, oxygen requirements, tolerance to hydrolysate inhibitors, and process temperature. Saccharomyces cerevisiae shows high ethanol tolerance but requires genetic modification for xylose use. Scheffersomyces stipitis ferments xylose naturally but lacks robustness. Kluyveromyces marxianus offers thermotolerance and a broad substrate range with lower ethanol yields, while O. polymorpha enables high-temperature fermentation but yields modest ethanol from xylose. The comparative analysis clarifies each yeast's advantages and limitations, supporting the development of more efficient 2 G bioethanol production strategies. Strain selection must balance ethanol yield, stress tolerance, and temperature adaptability to meet industrial requirements for cost-effective lignocellulosic bioethanol production.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12247168/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144559613","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

Image-based quantification of Candida albicans filamentation and hyphal length using the open-source visual programming language JIPipe. 使用开源可视化编程语言JIPipe对白色念珠菌丝状和菌丝长度进行图像量化。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf011

Jan-Philipp Praetorius, Sophia U J Hitzler, Mark S Gresnigt, Marc Thilo Figge

{"title":"Image-based quantification of Candida albicans filamentation and hyphal length using the open-source visual programming language JIPipe.","authors":"Jan-Philipp Praetorius, Sophia U J Hitzler, Mark S Gresnigt, Marc Thilo Figge","doi":"10.1093/femsyr/foaf011","DOIUrl":"10.1093/femsyr/foaf011","url":null,"abstract":"The formation of hyphae is one of the most crucial virulence traits the human pathogenic fungus Candida albicans possesses. The assessment of hyphal length in response to various stimuli, such as exposure to human serum, provides valuable insights into the adaptation strategies of C. albicans to the host environment. Despite the increasing high-throughput capacity live-cell imaging and data generation, the accurate analysis of hyphal growth has remained a laborious, error-prone, and subjective manual process. We developed an analysis pipeline utilizing the open-source visual programming language Java Image Processing Pipeline (JIPipe) to overcome the limitations associated with manual analysis of hyphal growth. By comparing our automated approach with manual analysis, we refined the strategies to achieve accurate differentiation between yeast cells and hyphae. The automated method enables length measurements of individual hyphae, facilitating a time-efficient, high-throughput, and user-friendly analysis. By utilizing this JIPipe analysis approach, we obtained insights into the filamentation behavior of two C. albicans strains when exposed to human serum albumin (HSA), the most abundant protein in human serum. Our findings indicate that despite the known role of HSA in stimulating fungal growth, it reduces filamentous growth. The implementation of our automated JIPipe analysis approach for hyphal growth represents a long-awaited and time-efficient solution to meet the demand of high-throughput data generation. This tool can benefit different research areas investigating the virulence aspects of C. albicans.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963753/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623946","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

Metabolic engineering of yeast to efficiently synthesize heme and hemoproteins: recent advance and prospects. 酵母高效合成血红素和血红蛋白的代谢工程研究进展与展望。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf019

Haibo Yu, Yunpeng Wang, Yijie Wang, Yueheng Niu, Jingwen Zhou, Jianghua Li, Jian Chen, Guocheng Du, Xinrui Zhao

引用次数: 0

Development of a yeast-based sensor platform for evaluation of ligands recognized by the human free fatty acid 2 receptor. 基于酵母的人体游离脂肪酸2受体识别配体传感器平台的开发。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf001

Andrea Clausen Lind, Davi De Castro Gomes, Ricardo Bisquert, Jonas Mårtensson, Martina Sundqvist, Huamei Forsman, Claes Dahlgren, Florian David, Verena Siewers

{"title":"Development of a yeast-based sensor platform for evaluation of ligands recognized by the human free fatty acid 2 receptor.","authors":"Andrea Clausen Lind, Davi De Castro Gomes, Ricardo Bisquert, Jonas Mårtensson, Martina Sundqvist, Huamei Forsman, Claes Dahlgren, Florian David, Verena Siewers","doi":"10.1093/femsyr/foaf001","DOIUrl":"10.1093/femsyr/foaf001","url":null,"abstract":"Yeast-based sensors have shown great applicability for deorphanization of G protein-coupled receptors (GPCRs) and screening of ligands targeting these. A GPCR of great interest is free fatty acid 2 receptor (FFA2R), for which short-chain fatty acids such as propionate and acetate are agonists. FFA2R regulates a wide array of downstream receptor signaling pathways in both adipose tissue and immune cells and has been recognized as a promising therapeutic target, having been implicated in several metabolic and inflammatory diseases. While research aiming to identify ligands recognized by FFA2R for translational applications is ongoing, screening is complicated by the complex regulatory and cell-specific responses mediated by the receptor. To simplify screening towards identification of novel ligands, heterologous platforms are valuable tools that offer efficient identification of ligand activity in the absence of regulatory mechanisms. Here, we present a yeast-based sensor designed to evaluate G protein α i1-mediated FFA2R signaling, with an assay time of 3 h. We verify this platform towards the natural agonists, propionate and acetate, and show applicability towards evaluation of synthetic agonists, antagonists, and allosteric agonists. As such, we believe that the developed yeast strain constitutes a promising screening platform for effective evaluation of ligands acting on FFA2R.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11781196/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143002734","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

Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing. 面向可持续生物制造的红圆菌木糖代谢途径工程。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf029

Hyunjoon Oh, Hyun Gi Koh, Suk-Chae Jung, Quanhui Ye, Sujit Sadashiv Jagtap, Christopher V Rao, Yong-Su Jin

{"title":"Engineering of xylose metabolic pathways in Rhodotorula toruloides for sustainable biomanufacturing.","authors":"Hyunjoon Oh, Hyun Gi Koh, Suk-Chae Jung, Quanhui Ye, Sujit Sadashiv Jagtap, Christopher V Rao, Yong-Su Jin","doi":"10.1093/femsyr/foaf029","DOIUrl":"10.1093/femsyr/foaf029","url":null,"abstract":"The oleaginous yeast Rhodotorula toruloides is a promising microbial cell factory for the sustainable production of biofuels and value-added chemicals from renewable carbon sources. Unlike the conventional yeast Saccharomyces cerevisiae, R. toruloides can naturally metabolize xylose, the second most abundant sugar in lignocellulosic hydrolysates. However, its native xylose metabolism is inefficient, characterized by slow xylose uptake and accumulation of D-arabitol. Moreover, despite its phenotype, research on the enzymes involved in xylose metabolism has yet to reach a consensus. Therefore, this review provides a comprehensive analysis of the non-canonical xylose metabolism in R. toruloides, focusing on the properties of key enzymes involved in xylose metabolism. Native xylose reductase and xylitol dehydrogenase exhibit broad substrate promiscuity compared to their counterparts in the xylose-fermenting Scheffersomyces stipitis. Additionally, the absence of xylulokinase expression under xylose-utilizing conditions redirects metabolism toward D-arabitol accumulation. Consequently, D-arabitol dehydrogenases and ribulokinase play essential roles in the xylose metabolism of R. toruloides. These findings highlight the fundamental differences between R. toruloides xylose metabolism and the oxidoreductase pathways observed in other xylose-fermenting yeast, providing insights for metabolic engineering strategies to improve xylose utilization and enhance bioconversion of cellulosic hydrolysates to different bioproducts by R. toruloides.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12199763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265814","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

Global transcription machinery engineering in Yarrowia lipolytica. 脂性耶氏菌的全球转录机械工程。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf023

Ewelina Celińska, Yongjin J Zhou

引用次数: 0

The experimentally evolved fluconazole-resistant clade II isolates of Candidozyma auris exhibit a distinct lipid compositional landscape, highlighting intraclade sphingolipid heterogeneity. 实验进化的抗氟康唑进化枝II型耳念珠菌分离株表现出独特的脂质组成景观，突出了进化枝内鞘脂的异质性。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf030

Praveen Kumar, Basharat Ali, Mohit Kumar, Hans Carolus, Celia Lobo Romero, Rudy Vergauwen, Anshu Chauhan, Aswathy Narayanan, Atanu Banerjee, Naseem A Gaur, Ashutosh Singh, Patrick Van Dijck, Arunaloke Chakrabarti, Shiva Prakash M Rudramurthy, Kaustuv Sanyal, Rajendra Prasad

{"title":"The experimentally evolved fluconazole-resistant clade II isolates of Candidozyma auris exhibit a distinct lipid compositional landscape, highlighting intraclade sphingolipid heterogeneity.","authors":"Praveen Kumar, Basharat Ali, Mohit Kumar, Hans Carolus, Celia Lobo Romero, Rudy Vergauwen, Anshu Chauhan, Aswathy Narayanan, Atanu Banerjee, Naseem A Gaur, Ashutosh Singh, Patrick Van Dijck, Arunaloke Chakrabarti, Shiva Prakash M Rudramurthy, Kaustuv Sanyal, Rajendra Prasad","doi":"10.1093/femsyr/foaf030","DOIUrl":"10.1093/femsyr/foaf030","url":null,"abstract":"The intrinsic resistance of Candidozyma auris (C. auris) to antifungal drugs poses a major therapeutic challenge, with conventional resistance mechanisms providing only partial explanations. Sphingolipids (SLs), known for their interclade heterogeneity, play a crucial role in antifungal resistance. This study examined the SL landscape in two drug-susceptible clade II isolates, C-line and P-line, from distinct geographical origins, which were experimentally evolved to develop stable fluconazole (FLC) resistance. The progenitors displayed distinct SL profiles, P1 had higher PhytoCer and αOHPhytoCer, indicating a more active acidic SL biosynthesis branch, whereas C1 exhibited elevated αOHGlcCer, αOHCer, and LCBs, reflecting a greater role of the neutral biosynthesis branch. The principal component analysis also confirmed distinct segregation of the two progenitors. Upon evolution, P1.1 and C1.1 adaptors showed significant SL alterations. P1.1 exhibited PhytoCer enrichment, while C1.1 showed reduced αOHGlcCer alongside increased PhytoCer, dhCer, and αOHPhytoCer levels. Notably, αOHGlcCer remained unchanged in P1.1, whereas LCBs and αOHPhytoCer decreased compared to P1. Despite these lineage-specific differences between the progenitors, both evolved replicates exhibited increased PhytoCer as a common denominator like what is also observed in clinical FLC-resistant isolates. These findings highlight intraclade SL variability and suggest that specific SLs contribute to FLC resistance in C. auris.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12203075/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire. 多嗜极酵母Naganishia friedmannii的基因组揭示了涉及应激反应途径，碳水化合物代谢扩展和有限DNA修复库的适应性。

IF 2.4 4区生物学

FEMS yeast research Pub Date : 2025-01-30 DOI: 10.1093/femsyr/foaf028

Lara Vimercati, Clifton P Bueno de Mesquita, Igor V Grigoriev, Sajeet Haridas, Steven K Schmidt, Alisha Quandt

{"title":"The genome of the polyextremophilic yeast, Naganishia friedmannii, reveals adaptations involved in stress response pathways, carbohydrate metabolism expansion, and a limited DNA repair repertoire.","authors":"Lara Vimercati, Clifton P Bueno de Mesquita, Igor V Grigoriev, Sajeet Haridas, Steven K Schmidt, Alisha Quandt","doi":"10.1093/femsyr/foaf028","DOIUrl":"10.1093/femsyr/foaf028","url":null,"abstract":"Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.","PeriodicalId":12290,"journal":{"name":"FEMS yeast research","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12204325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144233677","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