Root-associated fungi
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ABSTRACT:
PROVIDER: PRJNA473072 | ENA |
REPOSITORIES: ENA
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Project description:Cytosine methylation is a conserved base modification, but explanations for its interspecific variation remain elusive. Only through taxonomic sampling of disparate groups can unifying explanations for interspecific variation be thoroughly tested. Here we leverage phylogenetic resolution of cytosine DNA methyltransferases (DNA MTases) and genome evolution to better understand widespread interspecific variation across 40 diverse fungal species. DNA MTase genotypes have diversified from the ancestral DNMT1+DNMT5 genotype through numerous loss events, and duplications, whereas, DIM-2 and RID-1 are more recently derived in fungi. Methylation is typically enriched at intergenic regions, which includes repeats and transposons. Unlike certain Insecta and Angiosperm species, Fungi lack canonical gene body methylation. Some fungi species possess large clusters of contiguous methylation encompassing many genes, repetitive DNA and transposons, and are not ancient in origin. Broadly, methylation is partially explained by DNA MTase genotype and repetitive DNA content. Basidiomycota on average have the highest level of methylation, and repeat content, compared to other phyla. However, exceptions exist across Fungi. Other traits, including DNA repair mechanisms, might contribute to interspecific methylation variation within Fungi. Our results show mechanism and genome evolution are unifying explanations for interspecific methylation variation across Fungi.
2019-02-18 | GSE112636 | GEO
Project description:Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The oligonucleotides selected for fungal identification and the oligonucleotides specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory and food samples offering an interesting potential for microbiological laboratories. Keywords: Development of a diagnostic microarray for the identification of potentially mycotoxigenic fungi as well as genes leading to toxin production, 40 food-borne fungi, mycotoxins Development of a diagnostic array for the identification of food-borne fungi and their potential mycotoxin-producing genes. Oligonucleotide probes to be printed onto the array were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 α) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotides directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. Analysis was performed with 40 fungal cultures were obtained from the Agricultural Research Council culture collection (ARC), Pretoria, South Africa.an in-house spotted oligonucleotide microarray. The identity of each fungus was confirmed by standard laboratory procedures. For DNA isolation, the fungal strains were grown on 1.5% malt extract agar at 25°C for 1-2 weeks and total genomic fungal DNA was extracted following the DNA extraction protocol described by Raeder and Broda (1985). The internal transcribed spacer oligonucleotides ITS1, ITS3 and ITS4 were used as a reference for normalization of all spot intensity data.Samples were fluorescently labelled with Cy5 dye by using a Cyâ¢Dye Post-labelling Reactive Dye Pack and wre hybridized to the oligonucleotide microarray overnight. Two biological and one technical replicate (using independent labelling reactions) was performed, each replication consisting of a reverse labelling experiment.
2010-05-07 | E-GEOD-19227 | biostudies-arrayexpress
Project description:Mycotoxins are secondary metabolites which are produced by numerous fungi and pose a continuous challenge to the safety and quality of food commodities in South Africa. These toxins have toxicologically relevant effects on humans and animals that eat contaminated foods. In this study, a diagnostic DNA microarray was developed for the identification of the most common food-borne fungi, as well as the genes leading to toxin production. A total of 40 potentially mycotoxigenic fungi isolated from different food commodities, as well as the genes that are involved in the mycotoxin synthetic pathways, were analyzed. For fungal identification, oligonucleotide probes were designed by exploiting the sequence variations of the elongation factor 1-alpha (EF-1 alpha) coding regions and the internal transcribed spacer (ITS) regions of the rRNA gene cassette. For the detection of fungi able to produce mycotoxins, oligonucleotide probes directed towards genes leading to toxin production from different fungal strains were identified in data available in the public domain. The probes selected for fungal identification and the probes specific for toxin producing genes were spotted onto microarray slides. The diagnostic microarray developed can be used to identify single pure strains or cultures of potentially mycotoxigenic fungi as well as genes leading to toxin production in both laboratory samples and maize-derived foods offering an interesting potential for microbiological laboratories. Keywords: Development of a diagnostic microarray for the identification of potentially mycotoxigenic fungi as well as genes leading to toxin production, 40 food-borne fungi, mycotoxins
2010-03-01 | GSE19227 | GEO
Project description:Filamentous fungi are widely used in the production of biomass degrading enzymes, e.g. cellulases and pectinases. In order to study the secretome of biomass degrading fungi, proteomics studies were carried out on the extracellular proteins of fungal strains.
2024-01-03 | PXD048232 |
Project description:Plant pathogenic and beneficial fungi have evolved several strategies to evade immunity and cope with host-derived hydrolytic enzymes and oxidative stress in the apoplast, the extracellular spaces of plant tissues. Fungal hyphae are surrounded by an inner, insoluble cell wall layer and an outer, soluble extracellular polysaccharide (EPS) matrix. Here we show by proteomics and glycomics that these two layers have distinct protein and carbohydrate signatures, implicating different functions. The barley (Hordeum vulgare) β-1,3-endoglucanase HvBGLUII, which belongs to the widely distributed apoplastic GH17 family, is not active on fungal walls, but releases a conserved β-1,3;1,6-glucan decasaccharide (β-GD) from the EPS matrices of fungi with different lifestyles and taxonomic positions. This low molecular weight β-GD is resilient to further enzymatic hydrolysis by β-1,3-endoglucanases due to the presence of three β-1,6-linked glucose substituents and can scavenge reactive oxygen species via oxidative self-degradation. Additionally, exogenous application of β-GD leads to enhanced fungal colonization in barley. Our data highlights the hitherto undescribed capacity of this often-overseen fungal EPS layer to act as an outer protective barrier important for fungal accommodation within the hostile environment at the apoplastic plant-microbe interface.
2022-08-12 | PXD025640 | Pride
Project description:1. Research project objectives/Research hypothesis Phytopathogenic microfungi are plant parasites commonly found in the human environment. They may pose a potential threat to human health, as fungi are a generally known and prominent source of allergens. Allergic diseases are considered the epidemics of the twentieth century and are estimated to affect more than 30% of the population in industrialized countries with a still dramatically increasing incidence. However, the cause of existing allergies is not always identified by commonly used skin or blood tests. The essential allergenic fungi belong to the genera Alternaria, Aspergillus, Cladosporium, Penicillium, and Fusarium; however, it cannot be excluded that very common native and invasive phytopathogenic microfungi causing mass plant infestations are also a source of allergens. Therefore, we hypothesize that humans can inhale common phytopathogenic microfungi as a potential cause of allergic reactions. The subject of the research will be eight phytopathogenic microfungal species belonging to Erysiphales, Puccinales, Peronosporales, and Albuginales orders collected in their natural environment, comprehensive biochemical characteristics thereof, and determination of their potential impact on human asthma development. Both these species and their host plants are currently very common in Poland. The hosts include herbaceous plants, shrubs, planted species as well as ornamental plants or wild species that are very popular in parks and gardens. Phytopathogenic fungi cause massive infestation of plants and release vast amounts of spores. Such dissemination of plants and their parasites increases the risk of human contact with potential allergens. 2. Research project methodology Collected fungi will be identified both with microscopic and molecular methods (the fungal DNA sequences will be compared with relevant sequences available in the GenBank database with the use of the BLAST tool; also, a phylogenetic tree will be constructed using the MEGA7 program with the Neighbor-Joining method). We will carry out precise biochemical characteristics of fungal crude extracts; using the modern spectral methods will facilitate structural analysis of fatty acids and carbohydrates (gas-liquid chromatography-mass spectrometry) and protein identification (liquid chromatography-mass spectrometry). Fungal crude extracts will be used in in vitro studies to determine their cytotoxic potential in a human airway epithelial cell line and their ability to induce cytokines involved in allergic reactions – TNFα, TGFβ, GM-CSF, IL-1β, and IL-6. Based on in vitro results, chosen crude fungal extracts will induce acute and chronic asthma in a murine model (compared to positive controls – ovalbumin and Aspergillus fumigatus). We will study the remodeling of mouse lungs, serum IgE, and cytokine levels (IL-4, -5, -13, TNF-α, TGF-β), as well as the content of blood leukocytes (including eosinophils). 3. Expected impact of the research project on the development of science Prospective results will contribute to the extension of our basic knowledge about environmental threats to human health connected with native and invasive phytopathogenic microfungal species. Although many fungal allergens have been characterized in recent years, which proved very useful in diagnosing, the actual role of common and close-to-human plant parasites remains unknown. Biochemical characteristics of chosen microfungi will complete general knowledge about these still neglected plant parasites. At the same time, fatty acid profiles will be helpful to as chemotaxonomic markers for rapid identification and classification thereof. Additionally, including invasive plant parasites in our research has great significance not only for the Polish region but also for countries of their origin, which underlines the universal character of the presented project. Summing up, our research will cover a multi-faceted area: (i) taxonomy of microfungi – determination of rare in nature fungal components which will help in rapid classification thereof, (ii) molecular biology – genetic identification of fungal species, and identification of protein, fatty acids, and carbohydrates in inhaled fungal material with advanced spectroscopic methods, (iii) human health – indication of the allergic potential of phytopathogenic microfungi as a public health threat.
2025-06-25 | PXD058325 | Pride
Project description:We investigated the transcriptional response of invasive Mediterranean (MED) species of the whitefly B. tabaci complex (commonly referred to as Q biotype) to entomopathogenic fungi Beauveria bassiana using Illumina sequencing technology. Nearly 1,000 of control whiteflies, 48h fungal-induced whiteflies and 72h fungal-induced whiteflies were collected, respectively.
2013-11-24 | E-GEOD-38108 | biostudies-arrayexpress
Project description:The recent release of a large number of genomes from ectomycorrhizal, orchid mycorrhizal and root endophytic fungi have provided deep insight into fungal lifestyle-associated genomic adaptation. Comparative analyses of symbiotic fungal taxa showed that similar outcomes of interactions in distant related root symbioses are examples of convergent evolution. The order Sebacinales represents a sister group to the Agaricomycetes (Basidiomycota) that is comprised of ectomycorrhizal, ericoid-, orchid- mycorrhizal, root endophytic fungi and saprotrophs (Oberwinkler et al., 2013). Sebacinoid taxa are widely distributed from arctic to temperate to tropical ecosystems and are among the most common and species-rich groups of ECM, OM and endophytic fungi (Tedersoo et al., 2012, Tedersoo et al., 2010, Oberwinkler et al., 2013). The root endophyte Piriformospora indica and the orchid mycorrhizal fungus S. vermifera (MAFF 305830) are non-obligate root symbionts which were shown to be able to interact with many different experimental hosts, including the non-mycorrhizal plant Arabidopsis thaliana. These two fungi display similar colonization strategies in barley and in Arabidopsis and the ability to establish beneficial interactions with different hosts (Deshmukh et al., 2006). Colonization of the roots by P. indica and S. vermifera results in enhanced seed germination and biomass production as well as increased resistance against biotic and abiotic stresses in its experimental hosts, including various members of the Brassicaceae family, barley, Nicotiana attenuata and switchgrass (Ghimire, 2011, Ghimire et al., 2009, Ghimire et al., 2011, Waller et al., 2008, Barazani et al., 2007, Deshmukh et al., 2006). Microarray experiments were performed to identify and characterize conserved sebacinoid genes as key determinants in the Sebacinales symbioses.
2015-06-01 | GSE60736 | GEO
Project description:Ergosterol, a pivotal constituent of the fungal cell membrane, plays a crucial role in diverse cellular activities. Fungi inherently regulate ergosterol homeostasis, a process traditionally associated with the control of a major transcription factor, like SREBP, activated in response to ergosterol depletion, regardless of which ergosterol biosynthesis step is affected. Contrary to the established paradigm, our investigation demonstrates that the inhibition of ergosterol biosynthesis at specific steps triggers distinct transcriptional responses in erg genes across fungi, including Neurospora crassa, Aspergillus fumigatus, and Fusarium verticillioides. In N. crassa, the targeted responses are orchestrated by several transcription factors that have undergone functional rewiring. Specifically, ERG24 inhibition by amorolfine activates transcription factors SAH-2 and AtrR, resulting in the upregulation of erg24, erg2, erg25 and erg3. Additionally, ERG11 inhibition by azoles activates transcription factor NcSR, leading to the upregulation of erg11 and erg6. Our findings unveil a novel sophisticated regulation model of sterol biosynthesis in fungi which potentially enhances fungal survival in complex environments, thus providing new insights into sterol homeostasis maintenance and a deeper understanding of drug resistance mechanisms in fungi.
2024-03-24 | GSE261900 | GEO