Frontiers in fungal biology最新文献

{"title":"Antioxidant activity of mycelia methanolic extracts of endophytic fungi BvFV and BvFIX isolated from leaves of <i>Bauhinia variegata</i>.","authors":"Daniela Gurgel de Freitas Pires,&nbsp;Laíza Magalhães de Araújo,&nbsp;Pedro Góes Mesquita,&nbsp;Francisco de Assis Rocha Neves,&nbsp;Maria de Fátima Borin","doi":"10.3389/ffunb.2022.1048734","DOIUrl":"10.3389/ffunb.2022.1048734","url":null,"abstract":"<p><p>Endophytes are considered an essential source of natural products. Skin is the body's largest organ; its primary function is the protection of other organs, and aging is one of the most relevant problems associated with this organ. UV radiation generates reactive oxygen species (ROS), which lead to skin degeneration and consequent aging. The main endogenous antioxidants that neutralize ROS are enzymatic antioxidants such as superoxide dismutase (SOD), catalase, glutathione peroxidase, and glutathione reductase, and non-enzymatic antioxidants, such as glutathione and α-tocopherol. Nuclear receptors are involved in molecular mechanisms that control the aging process, especially peroxisome proliferator-activated receptors (PPAR), which regulate the function and expression of genes that modulate the balance between matrix metalloproteinases (MMP) activity and the expression of collagen. Some natural compounds, such as polyphenols, can activate PPAR and reduce the activation of MMP and collagen degradation. In this work, the antioxidant activity of the mycelia methanolic extracts of two endophytic fungi isolated from leaves of <i>Bauhinia variegata</i>, named BvFV and BvFIX, their action as PPAR agonists, and their effect on the activity of antioxidant defense system enzymes were evaluated. The mycelia methanolic extract of BvFV showed a weak agonist effect on PPARβ/δ, a high capability to inhibit lipid peroxidation, increased catalase activity, and increased superoxide dismutase activity by approximately 64%. In contrast, BvFIX increased catalase activity and increased superoxide dismutase activity in a dose-dependent manner, with an increase of 49.62% ± 7.87%, 56.64% ± 12.27%, and 240.46% ± 26.11% at concentrations of 25 µg/mL, 50 µg/mL and 100 µg/mL, respectively, in human dermal fibroblasts submitted to oxidative stress. These results suggest that the metabolites of the mycelia of endophytic fungi studied are promising to act in the chemoprevention of skin aging.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"1048734"},"PeriodicalIF":0.0,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512253/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A survey of <i>Fusarium</i> species and ADON genotype on Canadian wheat grain.","authors":"Janice Bamforth,&nbsp;Tiffany Chin,&nbsp;Tehreem Ashfaq,&nbsp;Niradha Withana Gamage,&nbsp;Kerri Pleskach,&nbsp;Sheryl A Tittlemier,&nbsp;Maria Antonia Henriquez,&nbsp;Shimosh Kurera,&nbsp;Sung-Jong Lee,&nbsp;Bhaktiben Patel,&nbsp;Tom Gräfenhan,&nbsp;Sean Walkowiak","doi":"10.3389/ffunb.2022.1062444","DOIUrl":"https://doi.org/10.3389/ffunb.2022.1062444","url":null,"abstract":"<p><strong>Introduction: </strong>Wheat is a staple food that is important to global food security, but in epidemic years, fungal pathogens can threaten production, quality, and safety of wheat grain. Globally, one of the most important fungal diseases of wheat is Fusarium head blight (FHB). This disease can be caused by several different <i>Fusarium</i> species with known differences in aggressiveness and mycotoxin-production potential, with the trichothecene toxin deoxynivalenol (DON) and its derivatives being of particular concern. In North America, the most predominant species causing FHB is <i>F. graminearum</i>, which has two distinct sub-populations that are commonly classified into two main chemotypes/genotypes based on their propensity to form trichothecene derivatives, namely 15-acetyldeoxynivalenol (15-ADON) and 3-acetyldeoxynivalenol (3-ADON).</p><p><strong>Materials and methods: </strong>We used a panel of 13 DNA markers to perform species and ADON genotype identification for 55, 444 wheat kernels from 7, 783 samples originating from across Canada from 2014 to 2020.</p><p><strong>Results and discussion: </strong>Based on single-seed analyses, we demonstrate the relationships between <i>Fusarium</i> species and trichothecene chemotype with sample year, sample location, wheat species (hexaploid and durum wheat), severity of <i>Fusarium</i> damaged kernels (FDK), and accumulation of DON. Results indicate that various <i>Fusarium</i> species are present across wheat growing regions in Canada; however, <i>F. graminearum</i> is the most common species and 3-ADON the most common genotype. We observed an increase in the occurrence of the 3-ADON genotype, particularly in the western Prairie regions. Our data provides important information on special-temporal trends in <i>Fusarium</i> species and chemotypes that can aid with the implementation of integrated disease management strategies to control the detrimental effects of this devastating disease.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"1062444"},"PeriodicalIF":0.0,"publicationDate":"2022-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Hortaea werneckii</i> isolates exhibit different pathogenic potential in the invertebrate infection model <i>Galleria mellonella</i>.","authors":"Stephanie Anthonies,&nbsp;José M Vargas-Muñiz","doi":"10.3389/ffunb.2022.941691","DOIUrl":"https://doi.org/10.3389/ffunb.2022.941691","url":null,"abstract":"<p><p><i>Hortaea werneckii</i> is a black yeast with a remarkable tolerance to salt. Most studies have been dedicated to understanding how <i>H. werneckii</i> adapts to hypersaline environments. <i>H. werneckii</i> has an unconventional cell cycle in which it alternates between fission and budding, which is modulated by cell density. Additionally, <i>H. werneckii</i> can cause superficial mycosis of the palm and sole of humans. Here, we determine the impact of salt concentration on the EXF-2000 strain's cell division pattern and morphology by performing timelapse microscopy at different salt concentrations. At low density and no salt, EXF-2000 primarily grows as pseudohyphae dividing mainly by septation. When grown in the presence of salt at a similar concentration to saltwater or hypersaline environments, we observe it grows first by undergoing fission followed by budding at the poles. Then, we examined a collection of 16 isolates in the presence of 0.6M NaCl, including isolates from marine and hypersaline environments and isolates from patients. These isolates exhibit a wide diversity in colony shape and cellular morphology. The isolates grew as yeast, pseudohyphae, and true hyphae, indicating that isolates can exhibit various cell morphologies under similar environmental conditions. We used the insect larvae <i>Galleria mellonella</i> to determine the pathogenic potential of our isolates. We observe that only a subset of isolates can cause death in our model, and there was no correlation between <i>H. werneckii</i> morphology and capacity to cause disease. Taken together, <i>H. werneckii</i> genomic and phenotypic diversity can serve as a model to better understand how phenotypes and pathogenic potential evolve in environmental fungi.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"941691"},"PeriodicalIF":0.0,"publicationDate":"2022-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512279/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41142036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Duration of the susceptibility of pruning wounds of different ages to infections by <i>Phaeomoniella chlamydospora</i> on grapevine cv. Cabernet Sauvignon in Central Chile.","authors":"Gonzalo A Díaz,&nbsp;Bernardo A Latorre","doi":"10.3389/ffunb.2022.1026516","DOIUrl":"10.3389/ffunb.2022.1026516","url":null,"abstract":"<p><p>Grapevine trunk diseases (GTDs) are one of the most important phytosanitary problems that affect grapevines (<i>Vitis vinifera</i>) worldwide. In Chile, <i>Phaeomoniella chlamydospora</i> is the major fungal trunk pathogen associated with GTDs. In the vineyards, the natural infections by <i>P. chlamydospora</i> are associated with air-borne conidia dispersed onto fresh pruning wounds from pycnidia. These pruning wounds are considered an important entrance for fungal trunk pathogens such as <i>P. chlamydospora</i> in the host in the field. However, the duration of the susceptibility of grapevine annual pruning wounds to <i>P. chlamydospora</i> is still unknown in Chile. Therefore, this study aimed to evaluate the period of susceptibility of pruning wounds of different ages to artificial infection of <i>P. chlamydospora</i> on grapevine cv. Cabernet Sauvignon, Central Chile. Artificial inoculations of a conidial suspension (10⁵ conidia/mL) of <i>P. chlamydospora</i> were used to determine the susceptibility of pruning wounds of different ages, from 1, 15, 30, and 45 days after pruning. The experiments were conducted on lignified cuttings in a greenhouse, and on vine spurs in two vineyards (Buin and Nancagua, Central Chile) during two consecutive seasons. The results indicated that the pruning wounds of grapevine cv. Cabernet Sauvignon were very susceptible to infections by <i>P. chlamydospora</i>, with a percentage of pruning wounds infected from 97 to 71% for cuttings, and 96% to 60% for spurs, during the first 15 days after pruning. However, the susceptibility of pruning wounds of different ages in cuttings and spurs of grapevine, generally decreased as the time from pruning to inoculation increased. Moreover, the pruning wounds the pruning wounds remained susceptible to artificial inoculation by <i>P. chlamydospora</i> for up 45 days after pruning with percent of wounds infected from 8.0 to 12.2, and 8.3 to 18.8% on cuttings and spurs of grapevine, respectively. Finally, this study constitutes study constitutes the first research focalized on the susceptibility of pruning wounds of various ages of grapevine cv. Cabernet Sauvignon to artificial inoculations by <i>P. chlamydospora</i> in Central Chile.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"1026516"},"PeriodicalIF":0.0,"publicationDate":"2022-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41157253","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tetraploidy accelerates adaptation under drug selection in a fungal pathogen.","authors":"Ognenka Avramovska,&nbsp;Amanda C Smith,&nbsp;Emily Rego,&nbsp;Meleah A Hickman","doi":"10.3389/ffunb.2022.984377","DOIUrl":"https://doi.org/10.3389/ffunb.2022.984377","url":null,"abstract":"<p><p>Baseline ploidy significantly impacts evolutionary trajectories and, specifically, tetraploidy is associated with higher rates of adaptation relative to haploidy and diploidy. While the majority of experimental evolution studies investigating ploidy use the budding yeast <i>Saccharomyces cerivisiae</i>, the fungal pathogen <i>Candida albicans</i> is a powerful system to investigate ploidy dynamics, particularly in the context of acquiring antifungal drug resistance. <i>C. albicans</i> laboratory and clinical strains are predominantly diploid, but have been isolated as haploid and polyploid. Here, we evolved diploid and tetraploid <i>C. albicans</i> for ~60 days in the antifungal drug caspofungin. Tetraploid-evolved lines adapted faster than diploid-evolved lines and reached higher levels of caspofungin resistance. While diploid-evolved lines generally maintained their initial genome size, tetraploid-evolved lines rapidly underwent genome-size reductions and did so prior to caspofungin adaptation. While clinical resistance was largely due to mutations in <i>FKS1</i>, these mutations were caused by substitutions in diploid, and indels in tetraploid isolates. Furthermore, fitness costs in the absence of drug selection were significantly less in tetraploid-evolved lines compared to the diploid-evolved lines. Taken together, this work supports a model of adaptation in which the tetraploid state is transient but its ability to rapidly transition ploidy states improves adaptive outcomes and may drive drug resistance in fungal pathogens.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"984377"},"PeriodicalIF":0.0,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Utilization of ferulic acid in <i>Aspergillus niger</i> requires the transcription factor FarA and a newly identified Far-like protein (FarD) that lacks the canonical Zn(II)₂Cys₆ domain.","authors":"Mark Arentshorst, Jos Reijngoud, Daan J C van Tol, Ian D Reid, Yvonne Arendsen, Herman J Pel, Noël N M E van Peij, Jaap Visser, Peter J Punt, Adrian Tsang, Arthur F J Ram","doi":"10.3389/ffunb.2022.978845","DOIUrl":"10.3389/ffunb.2022.978845","url":null,"abstract":"<p><p>The feruloyl esterase B gene (<i>faeB</i>) is specifically induced by hydroxycinnamic acids (e.g. ferulic acid, caffeic acid and coumaric acid) but the transcriptional regulation network involved in <i>faeB</i> induction and ferulic acid metabolism has only been partially addressed. To identify transcription factors involved in ferulic acid metabolism we constructed and screened a transcription factor knockout library of 239 <i>Aspergillus niger</i> strains for mutants unable to utilize ferulic acid as a carbon source. The <i>ΔfarA</i> transcription factor mutant, already known to be involved in fatty acid metabolism, could not utilize ferulic acid and other hydroxycinnamic acids. In addition to screening the transcription factor mutant collection, a forward genetic screen was performed to isolate mutants unable to express <i>faeB.</i> For this screen a <i>PfaeB-amdS</i> and <i>PfaeB-lux₆₁₃</i> dual reporter strain was engineered. The rationale of the screen is that in this reporter strain ferulic acid induces <i>amdS</i> (acetamidase) expression <i>via</i> the <i>faeB</i> promoter resulting in lethality on fluoro-acetamide. Conidia of this reporter strain were UV-mutagenized and plated on fluoro-acetamide medium in the presence of ferulic acid. Mutants unable to induce <i>faeB</i> are expected to be fluoro-acetamide resistant and can be positively selected for. Using this screen, six fluoro-acetamide resistant mutants were obtained and phenotypically characterized. Three mutants had a phenotype identical to the <i>farA</i> mutant and sequencing the <i>farA</i> gene in these mutants indeed showed mutations in FarA which resulted in inability to growth on ferulic acid as well as on short and long chain fatty acids. The growth phenotype of the other three mutants was similar to the <i>farA</i> mutants in terms of the inability to grow on ferulic acid, but these mutants grew normally on short and long chain fatty acids. The genomes of these three mutants were sequenced and allelic mutations in one particular gene (NRRL3_09145) were found. The protein encoded by NRRL3_09145 shows similarity to the FarA and FarB transcription factors. However, whereas FarA and FarB contain both the Zn(II)₂Cys₆ domain and a fungal-specific transcription factor domain, the protein encoded by NRRL3_09145 (FarD) lacks the canonical Zn(II)₂Cys₆ domain and possesses only the fungal specific transcription factor domain.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"978845"},"PeriodicalIF":2.1,"publicationDate":"2022-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512302/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41169025","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Genomic insights on fungal hybrids.","authors":"Toni Gabaldón,&nbsp;Chris Todd Hittinger","doi":"10.3389/ffunb.2022.1063609","DOIUrl":"10.3389/ffunb.2022.1063609","url":null,"abstract":"COPYRIGHT © 2022 Gabaldón and Hittinger. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Editorial PUBLISHED 07 November 2022 DOI 10.3389/ffunb.2022.1063609","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"1063609"},"PeriodicalIF":0.0,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41123547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small NRPS-like enzymes in <i>Aspergillus</i> sections <i>Flavi</i> and <i>Circumdati</i> selectively form substituted pyrazinone metabolites.","authors":"Matthew D Lebar,&nbsp;Brian M Mack,&nbsp;Carol H Carter-Wientjes,&nbsp;Qijian Wei,&nbsp;Christopher P Mattison,&nbsp;Jeffrey W Cary","doi":"10.3389/ffunb.2022.1029195","DOIUrl":"https://doi.org/10.3389/ffunb.2022.1029195","url":null,"abstract":"<p><p><i>Aspergillus</i> fungi produce mycotoxins that are detrimental to human and animal health. Two sections of aspergilli are of particular importance to cereal food crops such as corn and barley. <i>Aspergillus</i> section <i>Flavi</i> species like <i>A. flavus</i> and <i>A. parasiticus</i> produce aflatoxins, while section <i>Circumdati</i> species like <i>A. ochraceus</i> and <i>A. sclerotiorum</i> produce ochratoxin A. Mitigating these toxins in food and feed is a critical and ongoing worldwide effort. We have previously investigated biosynthetic gene clusters in <i>Aspergillus flavus</i> that are linked to fungal virulence in corn. We found that one such cluster, <i>asa</i>, is responsible for the production of aspergillic acid, an iron-binding, hydroxamic acid-containing pyrazinone metabolite. Furthermore, we found that the <i>asa</i> gene cluster is present in many other aflatoxin- and ochratoxin-producing aspergilli. The core gene in the <i>asa</i> cluster encodes the small nonribosomal peptide synthetase-like (NRPS-like) protein AsaC. We have swapped the <i>asaC</i> ortholog from <i>A. sclerotiorum</i> into <i>A. flavus</i>, replacing its native copy, and have also cloned both <i>asaC</i> orthologs into <i>Saccharomyces cerevisiae</i>. We show that AsaC orthologs in section <i>Flavi</i> and section <i>Circumdati</i>, while only containing adenylation-thiolation-reductase (ATR) domains, can selectively biosynthesize distinct pyrazinone natural products: deoxyaspergillic acid and flavacol, respectively. Because pyrazinone natural products and the gene clusters responsible for their production are implicated in a variety of important microbe-host interactions, uncovering the function and selectivity of the enzymes involved could lead to strategies that ultimately benefit human health.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"1029195"},"PeriodicalIF":0.0,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512218/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41159171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vacuolar proteases and autophagy in phytopathogenic fungi: A review.","authors":"Margarita Juárez-Montiel,&nbsp;Daniel Clark-Flores,&nbsp;Pedro Tesillo-Moreno,&nbsp;Esaú de la Vega-Camarillo,&nbsp;Dulce Andrade-Pavón,&nbsp;Juan Alfredo Hernández-García,&nbsp;César Hernández-Rodríguez,&nbsp;Lourdes Villa-Tanaca","doi":"10.3389/ffunb.2022.948477","DOIUrl":"https://doi.org/10.3389/ffunb.2022.948477","url":null,"abstract":"<p><p>Autophagy (macroautophagy) is a survival and virulence mechanism of different eukaryotic pathogens. Autophagosomes sequester cytosolic material and organelles, then fuse with or enter into the vacuole or lysosome (the lytic compartment of most fungal/plant cells and many animal cells, respectively). Subsequent degradation of cargoes delivered to the vacuole <i>via</i> autophagy and endocytosis maintains cellular homeostasis and survival in conditions of stress, cellular differentiation, and development. PrA and PrB are vacuolar aspartyl and serine endoproteases, respectively, that participate in the autophagy of fungi and contribute to the pathogenicity of phytopathogens. Whereas the levels of vacuolar proteases are regulated by the expression of the genes encoding them (e.g., <i>PEP4</i> for PrA and <i>PRB1</i> for PrB), their activity is governed by endogenous inhibitors. The aim of the current contribution is to review the main characteristics, regulation, and role of vacuolar soluble endoproteases and Atg proteins in the process of autophagy and the pathogenesis of three fungal phytopathogens: <i>Ustilago maydis</i>, <i>Magnaporthe oryzae</i>, and <i>Alternaria alternata</i>. Aspartyl and serine proteases are known to participate in autophagy in these fungi by degrading autophagic bodies. However, the gene responsible for encoding the vacuolar serine protease of <i>U. maydis</i> has yet to be identified. Based on <i>in silico</i> analysis, this <i>U. maydis</i> gene is proposed to be orthologous to the <i>Saccharomyces cerevisiae</i> genes <i>PRB1</i> and <i>PBI2</i>, known to encode the principal protease involved in the degradation of autophagic bodies and its inhibitor, respectively. In fungi that interact with plants, whether phytopathogenic or mycorrhizal, autophagy is a conserved cellular degradation process regulated through the TOR, PKA, and SNF1 pathways by ATG proteins and vacuolar proteases. Autophagy plays a preponderant role in the recycling of cell components as well as in the fungus-plant interaction.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"948477"},"PeriodicalIF":0.0,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41175947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"FunOrder 2.0 - a method for the fully automated curation of co-evolved genes in fungal biosynthetic gene clusters.","authors":"Gabriel A Vignolle,&nbsp;Robert L Mach,&nbsp;Astrid R Mach-Aigner,&nbsp;Christian Zimmermann","doi":"10.3389/ffunb.2022.1020623","DOIUrl":"https://doi.org/10.3389/ffunb.2022.1020623","url":null,"abstract":"<p><p>Coevolution is an important biological process that shapes interacting proteins - may it be physically interacting proteins or consecutive enzymes in a metabolic pathway, such as the biosynthetic pathways for secondary metabolites. Previously, we developed FunOrder, a semi-automated method for the detection of co-evolved genes, and demonstrated that FunOrder can be used to identify essential genes in biosynthetic gene clusters from different ascomycetes. A major drawback of this original method was the need for a manual assessment, which may create a user bias and prevents a high-throughput application. Here we present a fully automated version of this method termed FunOrder 2.0. In the improved version, we use several mathematical indices to determine the optimal number of clusters in the FunOrder output, and a subsequent k-means clustering based on the first three principal components of a principal component analysis of the FunOrder output to automatically detect co-evolved genes. Further, we replaced the BLAST tool with the DIAMOND tool as a prerequisite for using larger proteome databases. Potentially, FunOrder 2.0 may be used for the assessment of complete genomes, which has not been attempted yet. However, the introduced changes slightly decreased the sensitivity of this method, which is outweighed by enhanced overall speed and specificity.</p>","PeriodicalId":73084,"journal":{"name":"Frontiers in fungal biology","volume":"3 ","pages":"1020623"},"PeriodicalIF":0.0,"publicationDate":"2022-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10512238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41142037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}