Aspergillus flavus gene expression profile under different conditions of ustiloxin production
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PROVIDER: PRJNA561089 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome data of A. flavus was assembled under four different conditions (two strains and two media) for omics data analyses of genes related to ustiloxin production. The used two strains were the over-expressed strain (ustR-oe) of the transcription factor in ustiloxin gene cluster, ustR, and the pyrG marker complemented strain (control). The two media were V8 juice liquid and potato dextrose broth (PDB) media. The ustR-oe strain produced more ustiloxin B than the control strain, and the production is much higher in V8 than in PDB. Therefore, four different state of transcriptome could be obtained under these four conditions. The obtained transcriptome data was combined with the GEO data acc. no. GSE15435 and uesd for omics data analyses.
2020-04-17 | GSE136041 | GEO
Project description:To better understand the effect of temperature on mycotoxin biosynthesis, RNA-Seq technology was used to profile the Aspergillus flavus transcriptome under different temperature conditions. This approachallowed us to quantify transcript abundance for over 80% of fungal genes including 1,153 genes that were differentially expressed at 30°C and 37°C. Wleven of the 55 secondary metabolite clusters were up-regulated at the lower temperature, including aflatoxin biosynthesis genes, which were among the most highly up-expressed genes. On average, transcript abundance for the 30 aflatoxin biosynthesis genes was 3,300 times greater at 30°C as compared to 37°C. The results are consistent with the view that high temperature negatively affects aflatoxin production by turning down transcription of the two key transcriptional regulators, aflR and aflS. Subtle changes in the expression levels of aflS to aflR appear to control transcription activation of the aflatoxin cluster.
2011-06-16 | GSE30031 | GEO
Project description:To better understand the effect of temperature on mycotoxin biosynthesis, RNA-Seq technology was used to profile the Aspergillus flavus transcriptome under different temperature conditions. This approachallowed us to quantify transcript abundance for over 80% of fungal genes including 1,153 genes that were differentially expressed at 30M-BM-0C and 37M-BM-0C. Wleven of the 55 secondary metabolite clusters were up-regulated at the lower temperature, including aflatoxin biosynthesis genes, which were among the most highly up-expressed genes. On average, transcript abundance for the 30 aflatoxin biosynthesis genes was 3,300 times greater at 30M-BM-0C as compared to 37M-BM-0C. The results are consistent with the view that high temperature negatively affects aflatoxin production by turning down transcription of the two key transcriptional regulators, aflR and aflS. Subtle changes in the expression levels of aflS to aflR appear to control transcription activation of the aflatoxin cluster. 2 samples examined: from the fungus grown at 30M-BM-0C and 37M-BM-0C
2011-06-16 | E-GEOD-30031 | biostudies-arrayexpress
Project description:Aflatoxins are carcinogenic fungal secondary metabolites. Levels of aflatoxins in agricultural commodities are stringently regulated by many countries. A cluster of genes is responsible for aflatoxin biosynthesis by Aspergillus flavus and other closely related species. Expression of the clustered aflatoxin genes is governed by a complex network of regulatory mechanisms. To better understand the molecular events that are associated with aflatoxin production, transcription profiling by microarray analyses which compared three independent aflatoxigenic A. flavus strains to individual isogenic progenies that no longer produced aflatoxins after serial transfers was carried out. Twenty-two significantly differentially expressed features were identified. After physical mapping using the A. oryzae genome sequence as the reference, the number of unique genes was reduced to 16. Compared to the parental strains, changes in the aflatoxin gene expression levels in the progenies were not significant, which suggests that the inability to produce aflatoxins is not caused by decreased expression. The only gene showing higher expression levels in the progenies is homologous to glutathione S-transferease genes. Overexpression of this gene, named hcc, at six- to nine-fold in an aflatoxigenic A. flavus did not cause discernible changes in colony morphology or aflatoxin production. Loss of aflatoxin production after serial transfers may not result from a single event but caused by multiple factors. Keywords: Compartiave hybridization toxigenic and atoxigenic lines of Aspergillus Aspergillus flavus NRRL 29459, NRRL 29474, and NRRL 29490 are aflatoxigenic strains originated from soil collection in a peanut field (Terrell Co., Georgia, USA). Strains 459B-20-2, 474A-20, and 499A-20 were nonaflatoxigenic isolates obtained after 20 serial transfers of the parental strains on potato dextrose agar slants (Horn and Dorner 2002). Comparsions in each experiment consisted of one aflatoxigenic parental strain and one nonaflatoxigenic progeny, compared after 48- or 72-hr growth. Each comparison was repeated with duplicate dye-flip.
2010-05-26 | E-GEOD-8185 | biostudies-arrayexpress
Project description:Aspergillus flavus is the major producer of carcinogenic aflatoxins in crops worldwide. Natural populations of A. flavus show tremendous variation in aflatoxin production some of which can be attributed to extreme environmental conditions (e.g., drought), differential regulation of the aflatoxin biosynthetic pathway, missing cluster genes or loss-of-function mutations. Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative and qualitative differences in aflatoxigenicity. Several population studies provide indirect evidence of recombination in the aflatoxin gene cluster and genome-wide, using multilocus genealogical approaches. More recently A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses. In the present study, we characterize the progeny from nine A. flavus crosses and show that crossovers in the aflatoxin cluster coincide with inferred recombination blocks and hotspots in natural populations, which suggests that recombination in the cluster is primarily driven by sex. Moreover, we show that a single crossover event in the cluster can restore aflatoxigenicity, which is significant as mycotoxin production in A. flavus is highly heritable. aCGH was used to corroborate inferences from cluster-based MLSTs and to possibly identify additional crosovers within the cluster.
2012-03-07 | GSE27484 | GEO
Project description:Aflatoxins are toxic and carcinogenic secondary metabolites produced by the fungi Aspergillus flavus and A. parasiticus. In order to better understand the molecular mechanisms that regulate aflatoxin production, the biosynthesis of the toxin in A. flavus and A. parasticus grown in yeast extract sucrose media supplemented with 50 mM tryptophan (Trp) were examined. A. flavus grown in the presence of 50 mM tryptophan was found to have significantly reduced aflatoxin B1 and B2 biosynthesis, while A. parasiticus cultures had significantly increased B1 and G1 biosynthesis. Microarray analysis of RNA extracted from fungi grown under these conditions revealed seventy seven genes that are expressed significantly different between A. flavus and A. parasiticus, including the aflatoxin biosynthetic genes aflD (nor-1), aflE (norA), and aflO (omtB). It is clear that the regulatory mechanisms of aflatoxin biosynthesis in response to Trp in A. flavus and A. parasiticus are different. These candidate genes may serve as regulatory factors of aflatoxin biosynthesis. Keywords: Aflatoxin, Aspergillus, flavus, Amnio Acids, Tryptophan
2007-06-07 | GSE6182 | GEO
Project description:Aflatoxins are carcinogenic fungal secondary metabolites. Levels of aflatoxins in agricultural commodities are stringently regulated by many countries. A cluster of genes is responsible for aflatoxin biosynthesis by Aspergillus flavus and other closely related species. Expression of the clustered aflatoxin genes is governed by a complex network of regulatory mechanisms. To better understand the molecular events that are associated with aflatoxin production, transcription profiling by microarray analyses which compared three independent aflatoxigenic A. flavus strains to individual isogenic progenies that no longer produced aflatoxins after serial transfers was carried out. Twenty-two significantly differentially expressed features were identified. After physical mapping using the A. oryzae genome sequence as the reference, the number of unique genes was reduced to 16. Compared to the parental strains, changes in the aflatoxin gene expression levels in the progenies were not significant, which suggests that the inability to produce aflatoxins is not caused by decreased expression. The only gene showing higher expression levels in the progenies is homologous to glutathione S-transferease genes. Overexpression of this gene, named hcc, at six- to nine-fold in an aflatoxigenic A. flavus did not cause discernible changes in colony morphology or aflatoxin production. Loss of aflatoxin production after serial transfers may not result from a single event but caused by multiple factors. Keywords: Compartiave hybridization toxigenic and atoxigenic lines of Aspergillus
2008-06-18 | GSE8185 | GEO
Project description:Aspergillus flavus is the major producer of carcinogenic aflatoxins in crops worldwide. Natural populations of A. flavus show tremendous variation in aflatoxin production some of which can be attributed to extreme environmental conditions (e.g., drought), differential regulation of the aflatoxin biosynthetic pathway, missing cluster genes or loss-of-function mutations. Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative and qualitative differences in aflatoxigenicity. Several population studies provide indirect evidence of recombination in the aflatoxin gene cluster and genome-wide, using multilocus genealogical approaches. More recently A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses. In the present study, we characterize the progeny from nine A. flavus crosses and show that crossovers in the aflatoxin cluster coincide with inferred recombination blocks and hotspots in natural populations, which suggests that recombination in the cluster is primarily driven by sex. Moreover, we show that a single crossover event in the cluster can restore aflatoxigenicity, which is significant as mycotoxin production in A. flavus is highly heritable. aCGH was used to corroborate inferences from cluster-based MLSTs and to possibly identify additional crosovers within the cluster. aCGH comparison between 3 strains of A. flavus: 2 parental (P) and 1 progeny (F1) analyzed at the probe level. A total of 9 trio comparisons were made from a total of 18 isolates analyzed by aCGH. Trio comparisons are as follows: IC278 (P), IC1179 (P) and IC1650 (F1); IC201 (P), IC310 (P) and IC1719 (F1); IC307 (P), IC308 (P) and IC1751 (F1); IC277 (P), IC311 (P) and IC1766 (F1); IC277 (P), IC311 (P) and IC1775 (F1); IC244 (P), IC277 (P) and IC2205 (F1); IC244 (P), IC277 (P) and IC2207 (F1); IC301 (P), IC1179 (P) and IC2171 (F1); and finally IC244 (P), IC277 (P) and IC2209 (F1).
2012-03-07 | E-GEOD-27484 | biostudies-arrayexpress
Project description:Purpose: Aflatoxin B1 is the most toxic and carcinogenic compound in nature produced by Aspergillus fungi. In our study, we applied RNA-seq to compare the transcriptomic profiles of Aspergillus flavus strains in the presence and absence of medicinal plant Zanthoxylum bungeanum. Methods: mRNA profiles of Aspergillus flavus supplemented with 250 µg/ml of methanolic extract fraction (treated samples) or DMSO (control samples) were generated in triplicate, by an Illumina platform using paired-end 150 bp sequencing strategy. Clean paired-end reads were mapped to the reference genome of A. flavus NRRL3357. Gene expression quantification was calculated by FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced). The differentially expressed genes (DGEs) between the control and test samples were analyzed using the DESeq2 R package. Results: RNA-seq produced 24.5–32.1 million clean paired-end reads (150 bp read length) per sample and most of them (83–91%) were uniquely mapped to the reference genome of A. flavus NRRL3357. Eighty-two percent of genes displayed FPKM value ≥1 and were thus classified as expressed genes. Ninety-six percent of the expressed genes were expressed both in the control and test groups whereas 2.3% and 1.8% of the genes were expressed only in the control or test group, respectively. With the combination of FPKM fold change ≥2 and adjusted p-value <0.05, we found in total 950 DEG’s. Among them, 515 genes were downregulated and 435 genes were upregulated. We used FungiFun software to analyze the functions of the DEGs based on FunCat pathways and categories. About half of the DEG’s had a relevant annotation in the FunCat database, and 60–70% of the annotated DEG’s were found to be enriched in specific functional pathways. Conclusions: we showed that simple organic extracts from Z. bungeanum inhibit both the growth and aflatoxin production by Aspergillus flavus. The repression of AF pathway is mediated by global regulators instead of pathway specific regulators AflR or AflS. Consistently, the expression of Velvet complex, a prominent regulator of fungal secondary metabolism and development, was substantially reduced. Natural compound extracts from Z. bungeanum have potential to facilitate the development of safe and economical control strategies that shutdown aflatoxin production in aflatoxigenic Aspergillus species.
2022-04-10 | GSE179477 | GEO
Project description:The molecular mechanisms underlying aflatoxin production have been well-studied in strains of the fungus Aspergillus flavus (A. flavus) under artificial conditions. However, aflatoxin biosynthesis has rarely been studied in natural isolates of A. flavus strains. In the present study, tandem mass tag (TMT) labeling and high-performance liquid chromatography (HPLC) coupled with tandem-mass spectrometry analysiswere used for proteomic quantification in natural isolates of high- and low-aflatoxin-yield A. flavus strains.
2022-02-17 | PXD027517 | Pride