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PROVIDER: PRJNA1216263 | ENA |
REPOSITORIES: ENA
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Project description:Aspergillus flavus first gained scientific attention for its production of aflatoxin, the most potent naturally occurring toxin and hepatocarcinogenic secondary metabolite. For several decades, The DNA methylation status of A. flavus remains to be controversial. We first applied bisulfite sequencing, the gold standard at present, in conjunction with a biological replicate strategy to investigate the DNA methylation profiling of A. flavus genome. Our results reveal that the DNA methylation level of this fungus turns out to be negligible, comparable to the unmethylated lambda DNA we set as the false positive control of our bisulfite experiments. When comparing the DNA methyltransferase homolog of A. flauvs with that from several selected hypermethylated speices, we find that the DNA methyltransferase homolog of A.flavus as well as the other Aspergillus members groups closely with the RID from Neurospora crassa and Masc1 from Ascobolus immerses, which has been reported as DMT-incapable, but it diverges distantly from the other capable DNA methyltransferases. We observe significant depletion of repeat components within the A. flavus, which may possibly explain the lack of DNA methylation in this fungus. What's more, the RIP-index of the repeat of A. flavus turns out to be higher than the fungi without RID-like enzyme, suggesting this asexual fungus may possibly possess RIP process during the obscure sexual-stage which is very evanescent and may potentially related to DNA methylation. This work contributes to our understanding on the DNA methylation status of A. flavus. Also, it reinforces our views on the DNA methylation in fungal species. What's more, our strategy of applying bisulfite sequencing to DNA methylation detection on species with low DNA methylation may serve as a reference for later scientific investigations on other hypomethylated species. Two replicates were subjected to bisulfite conversion independently, unmethylated lambda DNA as a false positive control is added to both replicates.
2012-03-01 | E-GEOD-32177 | biostudies-arrayexpress
Project description:Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response. Included in the analysis are two biological replicates each of the fungus in buffer alone (control), the fungus challenged with wild type bacterium at 3 and 9 hours post-inoculation (hpi) and the fungus challeged with the mutant bacterium (mutated for ability to secrete antibiotics and enzymes) at 3 and 9 hpi.
2013-10-01 | E-GEOD-43648 | biostudies-arrayexpress
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus.
2014-04-01 | GSE54940 | GEO
Project description:Ectomycorrhizal fungi are dependent on host trees for carbon supply. In return ectomycorrhizal fungi supply trees with water and nutrients. It is known that when ectomycorrhizal fungi have exploited a nutrient rich patch in soil, the carbon allocation to mycelia in that patch is reduced, with the consequence of mycelia dying, but less is known of the dynamics of this senescence. We cultivated the ectomycorrhizal fungus Paxillus involutus in an axenic system. We collected growth and transcriptome data at different stages of carbon starvation during fungal growth. Carbon starvation induced a decrease in fungal biomass, which coincided with the release of NH4+ and the expression of genes connected with autophagy as well as protease and chitinase activity. Monoaromatic compounds, chitin and protease activity was detected in the liquid growth media during carbon starvation. The exudation of NH4+ and increase of monoaromatic compound during C starvation suggests senescence and autolysis of P. involutus. Together with the upregulation of genes involved in autophagy, chitinase and endopeptidase activity this points towards a controlled senescence including recycling of compounds originating from the fungi. Reduced C allocation to ectomycorrhizal mycelia in recently depleted nutrient patches in forest soils must be of ubiquitous nature. Understanding the mechanisms during exploitation of nutrients by ectomycorrhizal fungi is of great importance for understanding carbon and nutrient dynamics in forest soils. This is to our knowledge the first study describing the carbon starvation response in an ectomycorrhizal fungus. A one-chip study (data from 12 subarrays collected from a 12-plex Nimblegen microarray (ID 527890) using total RNA recovered from three separate glass-bead cultures of Paxillus involutus (ATCC200175) grown on Minimum Melin Norkrans medium (MMN) amended with ammonium (C/N ratio 3) and harvested at different times of carbon starvation.)
2014-04-01 | E-GEOD-54940 | biostudies-arrayexpress
Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
2017-08-02 | GSE85095 | GEO
Project description:The genus Collimonas consists of soil bacteria that are well known for their antifungal activity and for mycophagy, i.e. the ability to grow at the expense of living fungi. The aim of the current study was to gain a better understanding of the mechanisms of antagonism of Collimonas bacteria towards fungi, the involvement of the mycophagous phenotype, and the role of the fungus as a responsive partner in the interaction. In order to reach this aim, the bacterium Collimonas fungivorans and the fungus Aspergillus niger were confronted in vitro. Bacterial and fungal RNA were isolated at two time points during the interaction and analyzed by microarray analysis. Objective: Investigate the expression profile of a bacterium when it was challenged by the presence of an antagonist fungus (control was the expression profile of the bacterium when it was alone). In parallel investigate the expression profile of the antagonist fungus when it was challenged by the presence of the bacterium (control was the expression profile of the fungus when it was alone).(Additional file available in additional.zip)
2011-06-20 | E-MTAB-350 | biostudies-arrayexpress
Project description:Soil dwelling Aspergillus fungi possess the versatile metabolic capability to utilize complex organic compounds which are toxic to humans, yet the mechanisms they employ remain largely unknown. Benzo(a)pyrene is a common carcinogenic contaminant, posing a significant concern for human health. Here, we report that Aspergillus fungi can degrade benzo(a)pyrene effectively. In Aspergillus nidulans, exposure to benzo(a)pyrene results in transcriptomic and metabolic changes associated with cellular growth and energy generation, implying that the fungus utilizes benzo(a)pyrene as a food. Importantly, we identify and characterize the conserved bapA gene encoding a cytochrome P450 monooxygenase that exerts the first step in the degradation of benzo(a)pyrene. We further demonstrate that the fungal NF-κB-type global regulators VeA and VelB are required for benzo(a)pyrene degradation in A. nidulans, which occurs through expression control of bapA in response to nutrient limitation. Our study illuminates fundamental knowledge of fungal benzo(a)pyrene metabolism and provides novel insights into enhancing bioremediation potential.
2018-07-10 | GSE116804 | GEO
Project description:Plants and animals have evolved a first line of defense response to pathogens called innate or basal immunity. While basal defenses in these organisms are well studied, there is almost a complete lack of understanding of such systems in fungal species, and more specifically, how they are able to detect and mount a defense response upon pathogen attack. Hence, the goal of the present study was to understand how fungi respond to biotic stress by assessing the transcriptional profile of the rice blast pathogen, Magnaporthe oryzae, when challenged with the bacterial antagonist Lysobacter enzymogenes. Based on microscopic observations of interactions between M. oryzae and wild-type L. enzymogenes strain C3, we selected early and intermediate stages represented by time-points of 3 and 9 hours post-inoculation, respectively, to evaluate the fungal transcriptome using RNA-seq. For comparative purposes, we also challenged the fungus with L. enzymogenes mutant strain DCA, previously demonstrated to be devoid of antifungal activity. A comparison of transcriptional data from fungal interactions with the wild-type bacterial strain C3 and the mutant strain DCA revealed 463 fungal genes that were down-regulated during attack by C3; of these genes, 100 were also found to be up-regulated during the interaction with DCA. Functional categorization of genes in this suite included those with roles in carbohydrate metabolism, cellular transport and stress response. One gene in this suite belongs to the CFEM-domain class of fungal proteins. Another CFEM class protein called PTH11 has been previously characterized, and we found that a deletion in this gene caused advanced lesion development by C3 compared to its growth on the wild-type fungus. We discuss the characterization of this suite of 100 genes with respect to their role in the fungal defense response.
2013-10-01 | GSE43648 | GEO
Project description:The ascomycete fungus Beauveria bassiana is a pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. Genome-wide insight into the infection of the fungi is critical for genetic improvement of fungal insecticides but has been poorly explored. We constructed three transcriptomes of Beauveria bassiana at 24, 48 and 72 hours post treatment of infection (BbI) and of control (Bbc).
2017-04-18 | GSE97879 | GEO