Fungal Genetics and Biology最新文献_第2页

Characterization of a GH12 family glycosyl hydrolase from Neurospora crassa 粗神经孢子虫GH12家族糖基水解酶的研究。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-11-02 DOI: 10.1016/j.fgb.2025.104044

Protyusha Dey, Stephen J. Free

引用次数: 0

Association between genomic single nucleotide polymorphisms and susceptibility of Talaromyces marneffei 马尔尼菲Talaromyces marneffei基因组单核苷酸多态性与易感性的关系

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-11-22 DOI: 10.1016/j.fgb.2025.104046

Xiaofeng Li , Wenran Dan , Ming Luo , Peibo Li

{"title":"Association between genomic single nucleotide polymorphisms and susceptibility of Talaromyces marneffei","authors":"Xiaofeng Li , Wenran Dan , Ming Luo , Peibo Li","doi":"10.1016/j.fgb.2025.104046","DOIUrl":"10.1016/j.fgb.2025.104046","url":null,"abstract":"<div><div><em>Talaromyces marneffei</em> is a pathogenic fungus that causes talaromycosis. Although many antifungal drugs have been used for the treatment of talaromycosis, the effects of genomic mutations in different <em>T. marneffei</em> strains on the susceptibility to these antifungal drugs have not been fully studied. To reveal the association between genomic single nucleotide polymorphisms (SNPs) and susceptibility to <em>T. marneffei</em>, we sequenced the genomes of 15 clinical isolates of <em>T. marneffei</em> and analyzed the association between their SNPs and susceptibilities to 5-fluorouracil, anidulafungin, posaconazole, voriconazole, fluconazole, caspofungin, amphotericin B, micafungin, and itraconazole. A total of 87.29 Gb of sequencing reads were obtained from the 15 isolates, and 90,131 SNP loci were detected when compared to the reference genome of <em>T. marneffei</em>. Nine, one, one, and 14 SNP loci were potentially correlated with fluconazole, micafungin, posaconazole, and caspofungin susceptibilities, respectively. These results provide valuable genomic data for further analysis of drug resistance mechanisms and treatment strategies.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104046"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145598258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Classification and functional prediction of fungal glycosyltransferases using machine learning and deep learning methods 基于机器学习和深度学习方法的真菌糖基转移酶分类和功能预测。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-11-05 DOI: 10.1016/j.fgb.2025.104045

Alejandro Jose Gomez-Garcia, Jorge Humberto Ramirez-Prado

{"title":"Classification and functional prediction of fungal glycosyltransferases using machine learning and deep learning methods","authors":"Alejandro Jose Gomez-Garcia, Jorge Humberto Ramirez-Prado","doi":"10.1016/j.fgb.2025.104045","DOIUrl":"10.1016/j.fgb.2025.104045","url":null,"abstract":"<div><div>Glycosyltransferases (GTs) are ubiquitous multifunctional enzymes, responsible for catalyzing the transfer of sugar residues to generate structural diversity in biological systems. The extensive variability in structure, function, and mechanisms of action of GTs has resulted in multiple classification systems, hindering identification of significant patterns. This study aims to address this complexity by using machine learning and deep learning algorithms to uncover structural patterns associated to their function. A dataset of 3340 GTs from 88 representative fungal species across various divisions was utilized. Employing their predicted three-dimensional folding as well as their amino acid structural and biochemical characteristics, a Convolutional Variational Autoencoder (CVAE) model was used to summarize this information into five vectors, which were enriched with new derived variables and descriptive statistics. Cluster analysis and classification were conducted using the k-means algorithm to identify similarity patterns among the proteins. The clustering generated from enriched data exhibited greater coherence with the groups formed by k-means than the one generated solely from structural data. These findings demonstrated that the methodology employed, which integrates all variables in a unified manner, facilitates a comprehensive understanding of the relationships between GTs compared to approaches based on disparate criteria. The use of a CVAE, along with the innovative integration of biochemical and structural variables, resulted in a complementary and comprehensive, data-driven classification system of GTs. This approach represents a significant methodological advance beyond traditional sequence-based approaches as well as in the use of deep learning methodologies for the study of GTs and their biological functions.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104045"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145472448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

One hundred years of the Spitzenkörper: A story in three acts 百年spitzenkörper：三幕故事。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-09-13 DOI: 10.1016/j.fgb.2025.104036

Samantha V. González Téllez , Robert W. Roberson , Meritxell Riquelme

引用次数: 0

Abf1 participates in the response to DNA damage and replicative stress in Candida glabrata (Nakaseomyces glabratus) Abf1参与了光假丝酵母（Nakaseomyces glabratus）对DNA损伤和复制应激的反应。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-10-15 DOI: 10.1016/j.fgb.2025.104041

Laura Angélica Vera-Salazar, Grecia Hernández-Hernández, Guadalupe Gutiérrez-Escobedo, Alejandro De Las Peñas, Irene Castaño, Irene Castaño

{"title":"Abf1 participates in the response to DNA damage and replicative stress in Candida glabrata (Nakaseomyces glabratus)","authors":"Laura Angélica Vera-Salazar, Grecia Hernández-Hernández, Guadalupe Gutiérrez-Escobedo, Alejandro De Las Peñas, Irene Castaño, Irene Castaño","doi":"10.1016/j.fgb.2025.104041","DOIUrl":"10.1016/j.fgb.2025.104041","url":null,"abstract":"<div><div>ARS binding factor 1 (Abf1) is a DNA-binding protein found in various fungal species. In the opportunistic pathogenic fungus <em>Candida glabrata</em> (<em>Nakaseomyces glabratus</em>), Abf1 (CgAbf1) is encoded by the <em>ABF1</em> gene. Our research has demonstrated that CgAbf1 is essential for the viability of <em>C. glabrata</em> and is involved in the subtelomeric silencing of several <em>EPA</em> genes, which encode adhesins that mediate adhesion to epithelial cells, underscoring its significance as a virulence factor in this pathogen. Our previous findings established that both the depletion and overexpression of CgAbf1 result in growth defects and induce a delay in cell cycle progression. In this work, we wanted to determine if CgAbf1 is involved in the response to replicative and DNA damage stresses. We analyzed the CgAbf1 protein levels under these conditions and the activity of the Cg<em>ABF1</em> promoter and found that CgAbf1 negatively regulates its own transcription. A Bimolecular Fluorescence Complementation assay showed that CgAbf1 localizes to the nucleus and forms homodimers. We also found that CgAbf1 is involved in the survival to DNA damage caused by UV light and we demonstrated that <em>Saccharomyces cerevisiae</em> Abf1 (ScAbf1) can complement the lethality of the <em>C. glabrata abf1∆</em> strain.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104041"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145314370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Compound mutagenesis boosts β-carotene biosynthesis in Neurospora crassa: ATP synthase mutation and enzymes activities enhancement 复合诱变促进粗神经孢子虫β-胡萝卜素生物合成：ATP合酶突变及酶活性增强。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-10-04 DOI: 10.1016/j.fgb.2025.104040

Yue He , Qian Huang , Qingyang Lyu , Gaosheng Ji , Xinhui Wang , Zhiying Yan , Yijie Zhang , Xin Li , Xueping Tian

{"title":"Compound mutagenesis boosts β-carotene biosynthesis in Neurospora crassa: ATP synthase mutation and enzymes activities enhancement","authors":"Yue He , Qian Huang , Qingyang Lyu , Gaosheng Ji , Xinhui Wang , Zhiying Yan , Yijie Zhang , Xin Li , Xueping Tian","doi":"10.1016/j.fgb.2025.104040","DOIUrl":"10.1016/j.fgb.2025.104040","url":null,"abstract":"<div><div><em>Neurospora crassa</em> is a kind of biosafe fungus capable of synthesizing β-carotene from diverse feedstocks. However, the yield is constrained by the capacity of <em>N. crassa</em> strain. To improve the β-carotene synthesis ability, ultraviolet (UV), chemical (diethyl sulfate), and heavy ion beam were integratively employed in this study to breed <em>N. crassa</em> strain with high β-carotene producing performance. A mutant <em>N. crassa</em> strain exhibited 112.02 μg/g of β-carotene yield after 3 days fermentation, which was 325.5 % higher than initial strain. Subsequently, the key genes and metabolic pathways involved in β-carotene synthesis and substrates utilization was analyzed through whole-genome sequencing, and the results revealed that a synonymous nucleotide mutation on the ATPeV1A gene altered the RNA structure of ATP synthase and increased the ATP content. In addition, the significantly higher activities of protease, cellulase, and xylanase were observed in the mutant strain, further explained the speculation of high β-carotene yield.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104040"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Putative transcription factor Nrg1 is involved in the hyphal branching and the cell wall structure formation in the filamentous fungus Pleurotus ostreatus 据推测，转录因子Nrg1参与了丝状真菌平菇菌丝分支和细胞壁结构的形成。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-09-03 DOI: 10.1016/j.fgb.2025.104026

Saori Endo , Moriyuki Kawauchi , Yuitsu Otsuka , Junxian Han , Kenya Tsuji , Akira Yoshimi , Chihiro Tanaka , Shigekazu Yano , Takehito Nakazawa , Yoichi Honda

{"title":"Putative transcription factor Nrg1 is involved in the hyphal branching and the cell wall structure formation in the filamentous fungus Pleurotus ostreatus","authors":"Saori Endo , Moriyuki Kawauchi , Yuitsu Otsuka , Junxian Han , Kenya Tsuji , Akira Yoshimi , Chihiro Tanaka , Shigekazu Yano , Takehito Nakazawa , Yoichi Honda","doi":"10.1016/j.fgb.2025.104026","DOIUrl":"10.1016/j.fgb.2025.104026","url":null,"abstract":"<div><div>Nrg1 is a C2H2 zinc finger transcription factor that functions in various cellular processes related to environmental responses and cell wall synthesis in yeast. The present study investigated the function of Nrg1 in filamentous development in the white-rot fungus <em>Pleurotus ostreatus</em> for the first time. The Δ<em>nrg1</em> strains exhibited a higher frequency and larger angles of hyphal branching than the wild-type strain, suggesting <em>nrg1</em> is essential to hyphal branching regulation. Transmission electron microscopy observations indicated no significant change in cell wall thickness; however, the black layer on the cell wall surface, thought to be composed of proteins, including hydrophobins, was reduced. The reduced hydrophobin gene expression and hyphal hydrophobicity corroborate these observations. The <em>nrg1</em> disruption resulted in decreased levels of α-glucan and β-glucan content in the cell wall and the expression levels of their synthase genes. Fluorescent microscopy using protein probes for cell wall surface polysaccharides also suggested that in the Δ<em>nrg1</em> strains, there was an abnormal localization of chitin and β-glucan. In contrast, the fluorescent signals due to α-glucan and mannan were increased. These data demonstrate that Nrg1 is involved in the cell wall surface and structure formation via the gene expression of hydrophobin and polysaccharide synthases. This study provides the first evidence of the role of Nrg1 in filamentous fungi, especially in hyphal branching. It provides a clue toward a comprehensive understanding of the mechanisms regulating cell wall synthesis in white-rot fungi.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104026"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145007000","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Plasticity in initial infection traits in response to high temperature for worldwide representative Puccinia striiformis isolates 全球代表性纹状锈菌分离株初始侵染性状对高温响应的可塑性。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-09-26 DOI: 10.1016/j.fgb.2025.104039

Sajid Ali , Marc Leconte , Mogens S. Hovmøller , Jérôme Enjalbert , Claude de Vallavieille-Pope

{"title":"Plasticity in initial infection traits in response to high temperature for worldwide representative Puccinia striiformis isolates","authors":"Sajid Ali , Marc Leconte , Mogens S. Hovmøller , Jérôme Enjalbert , Claude de Vallavieille-Pope","doi":"10.1016/j.fgb.2025.104039","DOIUrl":"10.1016/j.fgb.2025.104039","url":null,"abstract":"<div><div>Limited knowledge is available regarding pathogen adaptation to environmental conditions, despite its importance to disease epidemiology. Wheat yellow rust, caused by the pathogen <em>Puccinia striiformis</em> offers an interesting case study, as the disease was so far considered limited to cool and humid climate, till the report of significant crop losses due to emergence of high temperature adapted lineages. We investigated the variability in temperature response in relationship with their genetic structure for 56 <em>P. striiformis</em> worldwide representative isolates including two isolates from the high temperature adapted strains <em>PstS1/S</em>2. High temperature adaptation was assessed through urediospore germination rate (GR) at 8 °C, 20 °C and 25 °C, and relative infection efficiency (RIE) measured at 20 °C, using two independent replicates of the experiments. Phylogenetic relations between isolates were based on 17 informative SSR markers, coinciding strongly with their geographical sampling origin. Variability was assessed considering populations (defined by sampling areas), where isolates from the pathogen centre of diversity in Himalayan region (Nepal and Pakistan) revealed adaptation to high temperatures in terms of germination rate and RIE, even higher than the reference <em>PstS1/S2</em> isolates, in comparison to isolates originating from cooler areas. The presence of high-temperature adapted isolates in genetically diverse populations of Asia (Nepal, Middle-East and Pakistan) represented an adaptation to local climate, where high temperature tolerance was correlated to the temperature of the sampling locations. Middle-East also represented variability for temperature responses. Following the genetic variability and plasticity of plant pathogens in reaction norm to temperature is therefore critical to forecast future epidemics in a global warming context.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104039"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Off-season sex in Zymoseptoria tritici: little room for late encounters 淡季的性活动：很少有晚相遇的空间

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-10-25 DOI: 10.1016/j.fgb.2025.104043

Frédéric Suffert, Manon Delanoue, Stéphanie Le Prieur, Alicia Noly

{"title":"Off-season sex in Zymoseptoria tritici: little room for late encounters","authors":"Frédéric Suffert, Manon Delanoue, Stéphanie Le Prieur, Alicia Noly","doi":"10.1016/j.fgb.2025.104043","DOIUrl":"10.1016/j.fgb.2025.104043","url":null,"abstract":"<div><div>This study complements a substantial body of experimental work on the model fungal pathogen <em>Zymoseptoria tritici</em> by exploring marginal processes and conditions of sexual reproduction. Recent findings have shown that avirulent strains can engage in sexual reproduction on resistant wheat plants, even when they fail to cause visible symptoms during the biotrophic phase. The objective was here to examine the (de)coupling of various processes operating during the epidemic period (living plants) and the interepidemic period (crop residues). We assessed whether various encounter scenarios between parental strains, involving co-inoculations performed either simultaneously or sequentially on living and dead wheat plants, could result in successful mating. A two-year experiment accounted for the compatibility between wheat varieties (one carrying the resistance gene <em>Stb16q</em>, the other not) and the strains (virulent or avirulent), and the nature of the inoculum (blastospores or pycnidiospores). The intensity of sexual reproduction was assessed for each scenario through quantification of ascospore production, complemented by genotyping of offspring to confirm their parental origin. The main result is that a <em>Z. tritici</em> strain arriving late on dead host tissues can still mate with a compatible strain that previously colonized the plant, whereas sexual reproduction does not occur if both strains arrive after the plant has dried. Quantitative analysis suggests that although matings initiated by late encounters on wheat residues are possible, they contribute very little to the overall offspring population (< 2 %). We discuss the epidemiological implications of this finding for disease management, highlighting both fundamental and applied questions it raises.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104043"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145466717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

The world of hyphae 第1章。菌丝的世界。

IF 2.3 3区生物学

Fungal Genetics and Biology Pub Date : 2025-12-01 Epub Date: 2025-09-12 DOI: 10.1016/j.fgb.2025.104033

Salomón Bartnicki-García

{"title":"The world of hyphae","authors":"Salomón Bartnicki-García","doi":"10.1016/j.fgb.2025.104033","DOIUrl":"10.1016/j.fgb.2025.104033","url":null,"abstract":"<div><div>This article describes the hyphal features that have allowed fungi to conquer nature so extensively and so ubiquitously. Fungi became champions of nutrition via absorption by developing hyphae with an efficient growth mechanism that combined rapid cell wall construction with secretion of digestive enzymes. Hyphae are long cylindrical cells growing at one end, the apex. Their cell walls are made by the combination of microfibrillar polymers (usually chitin) embedded in amorphous polysaccharides (usually β-1,3 glucans). Their high growth rate is supported by an efficient vesiclebased secretory apparatus, whose ultimate goal is to maintain a rapid flow of cell-wall building materials and digestive enzymes to the hyphal apex. The unique hyphoid morphology of a hypha can be described by a simple mathematic equation generated by a moving supply center emitting wall-building vesicles in all directions. The Spitzenkörper is proposed to function as a vesicle supply center that generates the characteristic cell wall of a hypha and also guides hyphal growth direction. Fungal organisms with completely different evolutionary origins, the cellulosic Oomycetes and the more numerous chitinous fungi, both develop hyphae and mycelia to insure efficient growth. Hyphae are thus the basis for the success of fungi in Nature.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"181 ","pages":"Article 104033"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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