A Network Approach of Gene Co-Expression in the Zea mays/Aspergillus flavus Pathosystem to Map Host/Pathogen Interaction Pathways
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: GSE85860
PROVIDER: PRJNA339565 | ENA |
REPOSITORIES: ENA
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Project description:A gene co-expression network was generated using a dual RNA-seq study with the fungal pathogen A. flavus and its plant host Z. mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network revealed a high degree of connectivity in many of the previously recognized pathways in Z. mays such as jasmonic acid, ethylene, and reactive oxygen species (ROS). For the pathogen A. flavus, a link between aflatoxin production and vesicular transport was identified within the network. There was significant interspecies correlation of expression between Z. mays and A. flavus for a subset of 104 Z. mays, and 1942 A. flavus genes. This resulted in an interspecies subnetwork enriched in multiple Z. mays genes involved in the production of reactive oxygen species. In addition to the ROS from Z. mays, there was enrichment in the vesicular transport pathways and the aflatoxin pathway for A. flavus. Included in these genes, a key aflatoxin cluster regulator, AflS, was found to be co-regulated with multiple Z. mays ROS producing genes within the network, suggesting AflS may be monitoring host ROS levels. The entire gene expression network for both host and pathogen, and the subset of interspecies correlations, is presented as a tool for hypothesis generation and discovery for events in the early stages of fungal infection of Z. mays by A. flavus.
2017-05-09 | GSE85860 | GEO
Project description: Not available
| S-EPMC5116468 | biostudies-literature
Project description:The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore authors undertook a systems biology approach involving dual RNA-seq to determine simultaneous response from the host and pathogen. What was dramatically highlighted in the analysis was upon infection there is uniformity in the development of the host and pathogen. This led to the development of host-pathogen index which was able to categorize the samples for down-stream system biology analysis. Additionally we were able to determine key genes in the pathways such as jasmonate, ethylene and ROS which were up-regulated in the studyThe stage of infection index used for the transcriptomic analysis revealed that A. flavus does not produce many transcripts initially during pathogenesis. It was found that when A. flavus was producing an abundance of transcripts, pathways involved the endosomal transport, aflatoxin production, sugar production and many others were up-regulated. In tandem, Z. mays had multiple resistance pathways, such as the phenylpropaniod, jasmonic acid and ethylene pathways that were up-regulated. The analysis of the gene regulatory networks revealed that multiple WRKY genes were targeting the activation of the resistance pathways. The analysis also revealed, for the first time, the activation of Z. mays resistance genes targeting A. flavus genes. Our results show that the plant-microbe interaction has multiple layers and that A. flavus transcriptionally reacts to the hostile environment of Z. mays. The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore authors undertook a systems biology approach involving dual RNA-seq to determine simultaneous response from the host and pathogen. What was dramatically highlighted in the analysis was upon infection there is uniformity in the development of the host and pathogen. This led to the development of host-pathogen index which was able to categorize the samples for down-stream system biology analysis. Additionally we were able to determine key genes in the pathways such as jasmonate, ethylene and ROS which were up-regulated in the studyThe stage of infection index used for the transcriptomic analysis revealed that A. flavus does not produce many transcripts initially during pathogenesis. It was found that when A. flavus was producing an abundance of transcripts, pathways involved the endosomal transport, aflatoxin production, sugar production and many others were up-regulated. In tandem, Z. mays had multiple resistance pathways, such as the phenylpropaniod, jasmonic acid and ethylene pathways that were up-regulated. The analysis of the gene regulatory networks revealed that multiple WRKY genes were targeting the activation of the resistance pathways. The analysis also revealed, for the first time, the activation of Z. mays resistance genes targeting A. flavus genes. Our results show that the plant-microbe interaction has multiple layers and that A. flavus transcriptionally reacts to the hostile environment of Z. mays. The interaction between Aspergillus flavus and Zea mays is complex, and the identification of plant genes and pathways conferring resistance to the fungus has been challenging. Therefore authors undertook a systems biology approach involving dual RNA-seq to determine simultaneous response from the host and pathogen. What was dramatically highlighted in the analysis was upon infection there is uniformity in the development of the host and pathogen. This led to the development of host-pathogen index which was able to categorize the samples for down-stream system biology analysis. Additionally we were able to determine key genes in the pathways such as jasmonate, ethylene and ROS which were up-regulated in the studyThe stage of infection index used for the transcriptomic analysis revealed that A. flavus does not produce many transcripts initially during pathogenesis. It was found that when A. flavus was producing an abundance of transcripts, pathways involved the endosomal transport, aflatoxin production, sugar production and many others were up-regulated. In tandem, Z. mays had multiple resistance pathways, such as the phenylpropaniod, jasmonic acid and ethylene pathways that were up-regulated. The analysis of the gene regulatory networks revealed that multiple WRKY genes were targeting the activation of the resistance pathways. The analysis also revealed, for the first time, the activation of Z. mays resistance genes targeting A. flavus genes. Our results show that the plant-microbe interaction has multiple layers and that A. flavus transcriptionally reacts to the hostile environment of Z. mays.
2020-06-14 | GSE101899 | GEO
Project description:Gel based proteomics of Aspergillus flavus
2013-05-30 | PRD000695 | Pride
Project description:Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and during storage. Previous studies indicate that both constitutive and induced resistance are involved in maize kernel defense against A. flavus infection, little is known about molecular mechanisms of mature kernels in response to fungal infection. The purpose of this study is to determine gene expression differences in maize kernels between resistant and susceptible lines in response to A. flavus challenge. To avoid the environmental effects in the field inoculation, a laboratory based inoculation technique Kernel Screening Assay (KSA) was used to challenge kernels with A. flavus. After 72 hours incubation of inoculated and noninculated mature kernels, gene expression profiles of two Near Isogenic Lines (NIL) of Eyl25 (A. flavus resistant) and Eyl31 (A. flavus susceptible) were compared using oligonucleotide array.
2010-10-01 | GSE19883 | GEO
Project description:Aflatoxin contamination caused by the opportunistic pathogen A. flavus is a major concern in maize production prior to harvest and during storage. Previous studies indicate that both constitutive and induced resistance are involved in maize kernel defense against A. flavus infection, little is known about molecular mechanisms of mature kernels in response to fungal infection. The purpose of this study is to determine gene expression differences in maize kernels between resistant and susceptible lines in response to A. flavus challenge. To avoid the environmental effects in the field inoculation, a laboratory based inoculation technique Kernel Screening Assay (KSA) was used to challenge kernels with A. flavus. After 72 hours incubation of inoculated and noninculated mature kernels, gene expression profiles of two Near Isogenic Lines (NIL) of Eyl25 (A. flavus resistant) and Eyl31 (A. flavus susceptible) were compared using oligonucleotide array. Direct comparisons were designed. The comparisons of NIL Eyl25 and Eyl31 include: Treated/Control, Control/Control and Treated/Treated. After 72 hours incubation under KSA conditions, forty seeds used in each A. flavus inoculated and noninculated group were bulked to extract total RNA. Four technical replications were performed in each comparison including two dye-swaps, total 16 hybridization reactions.
2010-10-01 | E-GEOD-19883 | biostudies-arrayexpress
Project description: Not available
| S-EPMC6963788 | biostudies-literature
Project description:Objective: Aspergillus flavus aflR, a gene encoding a Zn(II)2Cys6 DNA-binding domain, is an important transcriptional regulator of the aflatoxin biosynthesis gene cluster. Our previous results of GO analysis for the binding sites of AflR in A. flavus suggest that AflR may play an integrative regulatory role. This study aimed to investigate the integrative function of the aflR gene in A. flavus. Design: In this study, we used Aspergillus flavus NRRL3357 as a wild-type strain (WT) and constructed a knockout strain of A. flavus ΔaflR by homologous recombination. Based on the transcriptomics technology, we investigated the metabolic effects of aflR gene on growth, development and toxin synthesis of A. flavus, and discussed the overall regulation mechanism of aflR gene on A. flavus at the transcriptional level. Results: The disruption of aflR severely affected the aflatoxin biosynthetic pathway, resulting in a significant decrease in aflatoxin production. In addition, disrupted strains of the aflR gene produced relatively sparse conidia and a very small number of sclerotia. However, the biosynthesis of cyclopiazonic acid (CPA) was not affected by aflR gene disruption. Transcriptomic analysis of the ΔaflR strain grown on potato dextrose agar (PDA) plates at 0 h, 24 h, and 72 h showed that expression of clustering genes involved in the biosynthesis of aflatoxin was significantly down-regulated. Meanwhile, the ΔaflR strain showed significant expression differences in genes involved in spore germination, sclerotial development, and carbohydrate metabolism compared to the WT strain. Conclusions: The results showed that the A. flavus aflR gene also played a positive role in the growth and development of fungi.
2021-07-16 | GSE179978 | GEO
Project description:RNA-seq was used to compare differential gene expressions for Aspergillus flavus wild type strain and ASPES transcription factor deletion strains.The goals of this study are to explore the aflatoxin regulation pathway in A. flavus.
2018-12-25 | GSE107025 | 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