Pub Date : 2026-02-06DOI: 10.1016/j.fgb.2026.104068
Housong Cui, Li Zhang, Tong Liu, Runmao Lin
Fungal mitogenomes are significant for phylogenetic studies, however, constructing trees from full-length mitogenomes with varied sizes remains challenging. Recently, the dramatic increase of newly unannotated mitogenomes has created an urgent need for automated alignment tools. To address this, we developed WMAF, a novel Python-based tool that aligns full-length fungal mitogenomes by identifying and concatenating conserved genomic blocks. It overcomes recombination effects and prevents redundant locus detection. We further applied WMAF to five diverse genera, including Purpureocillium, Fusarium, Saccharomyces, Trichoderma, and Rhizoctonia, and generated mitochondrial trees that effectively identified intrageneric clades, as validated by nuclear trees. The method provides a foundation for advancing fungal phylogenetics and constructing the fungal tree of life.
{"title":"WMAF: One novel method for whole mitogenome alignment in fungi and its application in phylogenetic analysis.","authors":"Housong Cui, Li Zhang, Tong Liu, Runmao Lin","doi":"10.1016/j.fgb.2026.104068","DOIUrl":"https://doi.org/10.1016/j.fgb.2026.104068","url":null,"abstract":"<p><p>Fungal mitogenomes are significant for phylogenetic studies, however, constructing trees from full-length mitogenomes with varied sizes remains challenging. Recently, the dramatic increase of newly unannotated mitogenomes has created an urgent need for automated alignment tools. To address this, we developed WMAF, a novel Python-based tool that aligns full-length fungal mitogenomes by identifying and concatenating conserved genomic blocks. It overcomes recombination effects and prevents redundant locus detection. We further applied WMAF to five diverse genera, including Purpureocillium, Fusarium, Saccharomyces, Trichoderma, and Rhizoctonia, and generated mitochondrial trees that effectively identified intrageneric clades, as validated by nuclear trees. The method provides a foundation for advancing fungal phylogenetics and constructing the fungal tree of life.</p>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":" ","pages":"104068"},"PeriodicalIF":2.3,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146144688","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}
Pub Date : 2026-02-01DOI: 10.1016/j.fgb.2025.104054
Salomon Bartnicki-García, Meritxell Riquelme
{"title":"Hyphae: Tubular creators of the fungal kingdom","authors":"Salomon Bartnicki-García, Meritxell Riquelme","doi":"10.1016/j.fgb.2025.104054","DOIUrl":"10.1016/j.fgb.2025.104054","url":null,"abstract":"","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"182 ","pages":"Article 104054"},"PeriodicalIF":2.3,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745785","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}
Pub Date : 2026-01-25DOI: 10.1016/j.fgb.2026.104057
Tania Kurbessoian, David A Turissini, Patrick W Kelly, Oliver Kompathoum, Jonathan A Rader, Gaston I Jofre, Jingbaoyi Li, McKenna Sutherland, Victoria E Sepúlveda, Daniel R Matute
Histoplasma is a genus of human fungal pathogens that frequently affects immunosuppressed patients. Previous genetic surveys have largely focused on nucleotide-level variation, but much less attention has been given to more complex forms of mutation. Among these, transposable elements (TEs) represent an important class of mobile genetic elements that can alter genome size and play key roles in adaptation and speciation. In this study, we address this gap by examining the content and evolutionary dynamics of TEs in the human pathogen Histoplasma. Using previously published Histoplasma genome assemblies, we quantified TE content across eight phylogenetic species within the genus. Our analyses reveal heterogeneity in the evolutionary patterns of different TE families. The majority of TE orders and superfamilies show strong phylogenetic signal suggesting that phylogenetic relatedness significantly constrains the content of mobile genetic elements. We find no correlation between RNA or DNA TEs and genome size. Together, our results highlight the diverse landscape of TEs in Histoplasma and suggest that future studies should investigate their impact on genome evolution, fitness, and virulence.
{"title":"The dynamics of transposable element content in the genome of the human pathogen Histoplasma.","authors":"Tania Kurbessoian, David A Turissini, Patrick W Kelly, Oliver Kompathoum, Jonathan A Rader, Gaston I Jofre, Jingbaoyi Li, McKenna Sutherland, Victoria E Sepúlveda, Daniel R Matute","doi":"10.1016/j.fgb.2026.104057","DOIUrl":"10.1016/j.fgb.2026.104057","url":null,"abstract":"<p><p>Histoplasma is a genus of human fungal pathogens that frequently affects immunosuppressed patients. Previous genetic surveys have largely focused on nucleotide-level variation, but much less attention has been given to more complex forms of mutation. Among these, transposable elements (TEs) represent an important class of mobile genetic elements that can alter genome size and play key roles in adaptation and speciation. In this study, we address this gap by examining the content and evolutionary dynamics of TEs in the human pathogen Histoplasma. Using previously published Histoplasma genome assemblies, we quantified TE content across eight phylogenetic species within the genus. Our analyses reveal heterogeneity in the evolutionary patterns of different TE families. The majority of TE orders and superfamilies show strong phylogenetic signal suggesting that phylogenetic relatedness significantly constrains the content of mobile genetic elements. We find no correlation between RNA or DNA TEs and genome size. Together, our results highlight the diverse landscape of TEs in Histoplasma and suggest that future studies should investigate their impact on genome evolution, fitness, and virulence.</p>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":" ","pages":"104057"},"PeriodicalIF":2.3,"publicationDate":"2026-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146068528","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}
Trichosporon asahii is a dimorphic fungus that causes severe invasive fungal infections, particularly in patients with neutropenia. Depending on nutrient availability, T. asahii exists in yeast, hyphae, or arthroconidia forms. Atg1, a serine/threonine kinase, involves in stress responses and virulence in several fungi. The role of Atg1 in regulating morphology, stress resistance, or virulence in T. asahii, however, remains poorly understood. Here, we generated three atg1 gene-deficient T. asahii mutants and investigated their phenotypic characteristics to reveal the role of Atg1 in T. asahii. The atg1 gene-deficient mutants exhibited no growth defects under high-temperature or various chemical stress conditions, including antifungal drugs. The mutants exhibited an increased proportion of hyphal cells when cultured in Sabouraud dextrose broth (SB), a medium commonly used for fungi. On the other hand, no morphologic differences were observed between the parent strain and the atg1 gene-deficient mutants under a nitrogen-limited condition. The virulence of these atg1 gene-deficient mutants was maintained in a silkworm infection model. Furthermore, all three generated atg1 gene-deficient mutants exhibited consistent phenotypes. Our findings suggest that while Atg1 does not play a major role in stress tolerance or virulence in T. asahii under the tested conditions, it plays a role in regulating its dimorphic morphologic changes.
{"title":"Role of Atg1 in morphologic changes of the pathogenic fungus Trichosporon asahii","authors":"Mei Nakayama , Yasuhiko Matsumoto , Sanae Kurakado , Takashi Sugita","doi":"10.1016/j.fgb.2026.104058","DOIUrl":"10.1016/j.fgb.2026.104058","url":null,"abstract":"<div><div><em>Trichosporon asahii</em> is a dimorphic fungus that causes severe invasive fungal infections, particularly in patients with neutropenia. Depending on nutrient availability, <em>T. asahii</em> exists in yeast, hyphae, or arthroconidia forms. Atg1, a serine/threonine kinase, involves in stress responses and virulence in several fungi. The role of Atg1 in regulating morphology, stress resistance, or virulence in <em>T. asahii</em>, however, remains poorly understood. Here, we generated three <em>atg1</em> gene-deficient <em>T. asahii</em> mutants and investigated their phenotypic characteristics to reveal the role of Atg1 in <em>T. asahii</em>. The <em>atg1</em> gene-deficient mutants exhibited no growth defects under high-temperature or various chemical stress conditions, including antifungal drugs. The mutants exhibited an increased proportion of hyphal cells when cultured in Sabouraud dextrose broth (SB), a medium commonly used for fungi. On the other hand, no morphologic differences were observed between the parent strain and the <em>atg1</em> gene-deficient mutants under a nitrogen-limited condition. The virulence of these <em>atg1</em> gene-deficient mutants was maintained in a silkworm infection model. Furthermore, all three generated <em>atg1</em> gene-deficient mutants exhibited consistent phenotypes. Our findings suggest that while Atg1 does not play a major role in stress tolerance or virulence in <em>T. asahii</em> under the tested conditions, it plays a role in regulating its dimorphic morphologic changes.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"183 ","pages":"Article 104058"},"PeriodicalIF":2.3,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146044474","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}
Pub Date : 2025-12-18DOI: 10.1016/j.fgb.2025.104056
Judson Van Wyk , Xinxin Wang , Davis Mathieu , Gary L. Mills , Kevin L. Childs , Gregory Bonito
Morels (Morchella spp.) are iconic edible spring mushrooms renowned for their unique, meaty and earthy flavor profile. Wild-foraged morels are heavily relied upon to meet consumer demands, but optimizing cultivation is becoming critical as popularity continues to grow. The mating systems of Morchella spp. are of particular interest given their relevance to cultivation. Both heterothallic (outcrossing) and homothallic (self-fertile) life cycles have been reported. Here, we sequenced the genome of a commercial strain of Morchella rufobrunnea (GMI-8) to examine the genomic architecture surrounding the mating-type (MAT) loci and to provide a reference for transcriptomic analyses across its life cycle. To investigate gene regulation across developmental stages, we generated transcriptomes from six tissue types (sclerotia, mycelium, conidia, fundament, stipe, and hymenium) representing five key life stages. This sampling allowed us to profile the expression of mating-related, growth, and developmental associated genes across these life stages. Our analyses revealed a haploid genome size of 58 Mb, and co-localization of both MAT genes as required for sexual reproduction, confirming homothallism in this species. MAT genes (MAT1–1-1, 1–1-10, and 1–2-1) were highly expressed in conidial, fundament, and hymenial tissues, supporting the hypothesis that conidia may function as a nuclear donor/spermatia. This work improves our understanding of sexual reproduction and the life cycle of Morchella, and establishes a genomic and transcriptomic foundation for future studies of Morchella developmental biology.
{"title":"Life cycle transcriptomics of the homothallic cultivated morel (Morchella rufobrunnea)","authors":"Judson Van Wyk , Xinxin Wang , Davis Mathieu , Gary L. Mills , Kevin L. Childs , Gregory Bonito","doi":"10.1016/j.fgb.2025.104056","DOIUrl":"10.1016/j.fgb.2025.104056","url":null,"abstract":"<div><div>Morels (<em>Morchella</em> spp.) are iconic edible spring mushrooms renowned for their unique, meaty and earthy flavor profile. Wild-foraged morels are heavily relied upon to meet consumer demands, but optimizing cultivation is becoming critical as popularity continues to grow. The mating systems of <em>Morchella</em> spp. are of particular interest given their relevance to cultivation. Both heterothallic (outcrossing) and homothallic (self-fertile) life cycles have been reported. Here, we sequenced the genome of a commercial strain of <em>Morchella rufobrunnea</em> (GMI-8) to examine the genomic architecture surrounding the mating-type (MAT) loci and to provide a reference for transcriptomic analyses across its life cycle. To investigate gene regulation across developmental stages, we generated transcriptomes from six tissue types (sclerotia, mycelium, conidia, fundament, stipe, and hymenium) representing five key life stages. This sampling allowed us to profile the expression of mating-related, growth, and developmental associated genes across these life stages. Our analyses revealed a haploid genome size of 58 Mb, and co-localization of both MAT genes as required for sexual reproduction, confirming homothallism in this species. MAT genes (MAT1–1-1, 1–1-10, and 1–2-1) were highly expressed in conidial, fundament, and hymenial tissues, supporting the hypothesis that conidia may function as a nuclear donor/spermatia. This work improves our understanding of sexual reproduction and the life cycle of <em>Morchella,</em> and establishes a genomic and transcriptomic foundation for future studies of <em>Morchella</em> developmental biology.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"182 ","pages":"Article 104056"},"PeriodicalIF":2.3,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800862","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}
Pub Date : 2025-12-11DOI: 10.1016/j.fgb.2025.104055
Victoria Pommer , Renan do Nascimento Barbosa , Felipe Geremia , Igor Daniel Alves , Matheus da Silva Camargo , Esther Maria Rocha , Nicolau Sbaraini , Charley Staats , Cristina Maria de Souza-Motta , Augusto Schrank , Marilene Henning Vainstein
The genus Periconia is recognized for its ability to produce several organic compounds with biotechnological potential. Despite the importance of these fungi, genomic studies on Periconia species remain limited. In this study, we performed a morphological and whole-genome sequence characterization of Periconia belmontensis sp. nov. isolated from the São Pedro and São Paulo Archipelago, Brazilian oceanic islets at the Mid-Atlantic Ridge. Our results indicate that potato dextrose agar and malt extract agar are optimal for fungal growth at 28 °C. Multilocus phylogenetic analysis and morphological characters support the establishment of the new species. Genome sequence assembly revealed a genome size of 50 Mb, whereas secondary metabolite analysis identified fifty putative biosynthetic gene clusters (BGCs). Gene conservation analysis revealed 1856 unique genes, mainly related to capturing and processing nutrient activity, compared with four others available Periconia genomes. The present study contributes to the expansion of molecular databases for Periconia. These findings also assist in silico exploration of novel molecules and increase the understanding of the biotechnological potential of these species.
Periconia属因其生产几种具有生物技术潜力的有机化合物的能力而被认可。尽管这些真菌很重要，但对这些真菌的基因组研究仍然有限。在这项研究中，我们进行了从巴西大西洋中山脊的岛屿 o Pedro和 o Paulo群岛分离的Periconia belmontensis sp. 11 .的形态学和全基因组序列表征。我们的研究结果表明，马铃薯葡萄糖琼脂和麦芽提取物琼脂在28 °C时最适合真菌生长。多位点系统发育分析和形态学特征支持新种的建立。基因组序列组装显示基因组大小为50 Mb，而次级代谢物分析鉴定了50个假定的生物合成基因簇（bgc）。基因保守分析结果显示，与其他4个水仙花基因组相比，共有1856个独特基因，主要与捕获和处理营养活性有关。本文的研究有助于扩大水蛭属植物的分子数据库。这些发现还有助于对新分子的硅探索，并增加对这些物种生物技术潜力的理解。
{"title":"Fungi from Brazilian Oceanic Islands: Identification and genome characterization of Periconia belmontensis sp. nov. isolated from São Pedro and São Paulo archipelago","authors":"Victoria Pommer , Renan do Nascimento Barbosa , Felipe Geremia , Igor Daniel Alves , Matheus da Silva Camargo , Esther Maria Rocha , Nicolau Sbaraini , Charley Staats , Cristina Maria de Souza-Motta , Augusto Schrank , Marilene Henning Vainstein","doi":"10.1016/j.fgb.2025.104055","DOIUrl":"10.1016/j.fgb.2025.104055","url":null,"abstract":"<div><div>The genus <em>Periconia</em> is recognized for its ability to produce several organic compounds with biotechnological potential. Despite the importance of these fungi, genomic studies on <em>Periconia</em> species remain limited. In this study, we performed a morphological and whole-genome sequence characterization of <em>Periconia belmontensis</em> sp. nov. isolated from the São Pedro and São Paulo Archipelago, Brazilian oceanic islets at the Mid-Atlantic Ridge. Our results indicate that potato dextrose agar and malt extract agar are optimal for fungal growth at 28 °C. Multilocus phylogenetic analysis and morphological characters support the establishment of the new species. Genome sequence assembly revealed a genome size of 50 Mb, whereas secondary metabolite analysis identified fifty putative biosynthetic gene clusters (BGCs). Gene conservation analysis revealed 1856 unique genes, mainly related to capturing and processing nutrient activity, compared with four others available <em>Periconia</em> genomes. The present study contributes to the expansion of molecular databases for <em>Periconia</em>. These findings also assist in silico exploration of novel molecules and increase the understanding of the biotechnological potential of these species.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"182 ","pages":"Article 104055"},"PeriodicalIF":2.3,"publicationDate":"2025-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745834","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}
Pub Date : 2025-12-01DOI: 10.1016/j.fgb.2025.104046
Xiaofeng Li , Wenran Dan , Ming Luo , Peibo Li
Talaromyces marneffei 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 T. marneffei 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 T. marneffei, we sequenced the genomes of 15 clinical isolates of T. marneffei 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 T. marneffei. 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.
{"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}
Pub Date : 2025-11-25DOI: 10.1016/j.fgb.2025.104047
Meareg G. Amare , Miette K. Hennessy , Grant Nickles , Sung Chul Park , Sachin Jain , Neta Shlezinger , Nancy P. Keller , Mehdi Kabbage
Regulated cell death (RCD) is a highly conserved and coordinated cellular demise process. In animals, the fate of cells depends on the precise regulation of RCD, with inhibitors of apoptosis proteins (IAPs) playing a major role as negative regulators of cellular death. In fungi, RCD regulates crucial processes, including growth, development, stress response, host-pathogen interactions and more. However, the biochemical details of this process are not well understood in this kingdom. IAPs are, remarkably, one of the few RCD/Apoptosis-regulatory proteins that are conserved in fungi. Here, we performed large-scale bioinformatic analyses of IAPs in sequenced fungal genomes. While most fungal organisms have a single IAP gene (81.65 % of the genomes analyzed here), some fungi lack IAPs altogether and others have multiple IAP-like genes. Using the Aspergillus nidulans IAP, AnBir1, we show that this protein is required for survival and regulates cell death by inhibiting caspase-like activity. Moreover, disrupting RCD by constitutively expressing AnBir1 impacted fundamental processes, including development, stress response and secondary metabolism. We also show that fungal RCD can be hijacked for therapeutic purposes. Using virus-induced gene silencing (VIGS), we targeted the AnBir1 homolog of the plant pathogenic fungus Sclerotinia sclerotiorum (SsBir1) during plant infection. Targeting SsBir1 resulted in enhanced resistance to S. sclerotiorum infection. We propose that IAPs play a critical role in regulating caspase activities and other RCD-related processes in fungi and may constitute a novel therapeutic target for fungal infections.
{"title":"AnBir1: a conserved fungal inhibitor of apoptosis regulates caspase activity and core processes in Aspergillus nidulans","authors":"Meareg G. Amare , Miette K. Hennessy , Grant Nickles , Sung Chul Park , Sachin Jain , Neta Shlezinger , Nancy P. Keller , Mehdi Kabbage","doi":"10.1016/j.fgb.2025.104047","DOIUrl":"10.1016/j.fgb.2025.104047","url":null,"abstract":"<div><div>Regulated cell death (RCD) is a highly conserved and coordinated cellular demise process. In animals, the fate of cells depends on the precise regulation of RCD, with inhibitors of apoptosis proteins (IAPs) playing a major role as negative regulators of cellular death. In fungi, RCD regulates crucial processes, including growth, development, stress response, host-pathogen interactions and more. However, the biochemical details of this process are not well understood in this kingdom. IAPs are, remarkably, one of the few RCD/Apoptosis-regulatory proteins that are conserved in fungi. Here, we performed large-scale bioinformatic analyses of IAPs in sequenced fungal genomes. While most fungal organisms have a single IAP gene (81.65 % of the genomes analyzed here), some fungi lack IAPs altogether and others have multiple IAP-like genes. Using the <em>Aspergillus nidulans</em> IAP, AnBir1, we show that this protein is required for survival and regulates cell death by inhibiting caspase-like activity. Moreover, disrupting RCD by constitutively expressing AnBir1 impacted fundamental processes, including development, stress response and secondary metabolism. We also show that fungal RCD can be hijacked for therapeutic purposes. Using virus-induced gene silencing (VIGS), we targeted the AnBir1 homolog of the plant pathogenic fungus <em>Sclerotinia sclerotiorum</em> (SsBir1) during plant infection. Targeting SsBir1 resulted in enhanced resistance to <em>S. sclerotiorum</em> infection. We propose that IAPs play a critical role in regulating caspase activities and other RCD-related processes in fungi and may constitute a novel therapeutic target for fungal infections.</div></div>","PeriodicalId":55135,"journal":{"name":"Fungal Genetics and Biology","volume":"182 ","pages":"Article 104047"},"PeriodicalIF":2.3,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145642839","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}
Pub Date : 2025-11-05DOI: 10.1016/j.fgb.2025.104045
Alejandro Jose Gomez-Garcia, Jorge Humberto Ramirez-Prado
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.
{"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":"2025-11-05","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}
Pub Date : 2025-11-02DOI: 10.1016/j.fgb.2025.104044
Protyusha Dey, Stephen J. Free
The Neurospora crassa genome encodes a single glycosyl hydrolase family 12 enzyme GH12–1. To characterize the enzyme, the gh12–1 gene was cloned and tagged with a HIS6 tag. Characterization of the purified GH12–1 enzyme showed that it cleaves carboxymethylcellulose, laminarin (β-1,3-glucan) and lichenin (a mixed β-1,3−/β-1,4-glucan) to release trisaccharides from an end of the polysaccharide substrate. Laminarin and lichenin are the major polysaccharides found in the N. crassa cell wall. We conclude that GH12–1 could function to degrade cellulose and/or to digest laminarin and lichenin polysaccharides released from the cell wall during cell wall remodeling.
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