Time series transcriptional profiling of Ustilago maydis SG200 infecting Zea mays.
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ABSTRACT:
PROVIDER: PRJNA506360 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8224520_1.fastq.gz | Fastqsanger.gz | |||
| SRR8224520_2.fastq.gz | Fastqsanger.gz | |||
| SRR8224521_1.fastq.gz | Fastqsanger.gz | |||
| SRR8224521_2.fastq.gz | Fastqsanger.gz | |||
| SRR8224522_1.fastq.gz | Fastqsanger.gz |
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Project description:Goals: Comparing the infection between Ustilago maydis SG200 with the wild-type strain FB1xFB2 previously published Methods: Comparative RNASeq analysis between U. maydis SG200 and U. maydis FB1xFB2 at three timepoints (axenic, 2dpi, 12dpi) Results: The RNASeq analysis in SG200 identifies differences in gene expression with FB1xFB2. These differences could be the result of a unequal contribution of each nuclei to transcription. Further analysis identified a set of differentially transcribed genes.
2022-12-24 | GSE122788 | GEO
Project description:Time series transcriptional profiling of Ustilago maydis infecting Zea mays
| PRJNA407369 | ENA
Project description:The basidiomycete fungus Ustilago maydis causes smut disease in maize and has become an important model for elucidating the strategies used for host colonization by biotrophic fungi. In this study, we performed an in-depth transcriptional profiling of the plant-associated development of a cross between U. maydis FB1 and FB2 wildtype strains. The analysis of eight different stages, including the development on the leaf surface, early colonization, tumor induction and spore maturation, offers an unprecedented view of the changes in the fungal transcriptome associated with the passage through the entirely biotrophic life cycle. In our analysis, we focus on fungal metabolism, nutritional strategies, secreted effectors and regulatory networks. Secreted proteins were enriched in three distinct expression modules corresponding to the plant surface, establishment of biotrophy and tumor formation, respectively. These modules are likely the key determinants for U. maydis virulence. With respect to nutrient utilization, we observed that expression of several nutrient transporters was tied to these virulence modules rather than being controlled by nutrient availability. We show that oligopeptide transporters likely involved in nitrogen supply during infection are important virulence determinants. By measuring the intramodular connectivity of transcription factors, we identified potential drivers for the virulence modules. While known components of the b-cascade served as inducers for the plant surface and biotrophy module, we identified a set of yet uncharacterized transcription factors as likely responsible for expression of the tumor module. We demonstrate a crucial role in effector gene expression and tumor formation for one of these transcription factors.
2018-01-11 | GSE103876 | GEO
Project description:Zea mays transcriptome profiling of infected seedlings by the Ustilago maydis wildtype and the seedling specific effector mutant demonstrated the variation of gene expression in the mutant and the classes of genes that are absent in the mutant as compared to the wildtype U. maydis SG200 strain. Two dye competitive hybridizations were performed on Agilent Oligo arrays.
2015-03-09 | GSE63077 | GEO
Project description:Gene expression of Ustilago maydis SG200, SG200∆hxt1 and the avirulent SG200∆hxt1 hxt1(R164K) on maize leaf surface
| PRJNA260180 | ENA
Project description:The fungal pathogen Ustilago maydis establishes a biotrophic relationship with its host plant maize. Hallmarks of the disease are large plant tumors in which fungal proliferation occurs. Plants have developed various defense pathways to cope with pathogens. We used microarrays to detail the global programme of gene expression during the infection process of Ustilago maydis in its host plant to get insights into the defense programs and the metabolic reprogramming needed to supply the fungus with nutrients. Experiment Overall Design: In three independent experiments plants were infected with the solopathogenic U. maydis strain SG200. Samples from infected leaves were taken at 12 and 24 hours post infection, as well as 2, 4 and 8 days post infection. Samples from uninfected control plants were taken at the same time points.
2008-04-07 | E-GEOD-10023 | biostudies-arrayexpress
Project description:Anthocyanin induction in plant is considered a general defense response against biotic and abiotic stresses. The infection by Ustilago maydis, the corn smut pathogen, is accompanied with anthocyanin induction in leaf tissue. We revealed that anthocyanin is intentionally induced by the virulence promoting secreted effector protein Tin2. Tin2 protein functions inside plant cells where it interacts with cytoplasmic maize protein kinase ZmTTK1. Tin2 masks an ubiquitin-proteasome degradation motif in ZmTTK1 leading to a more stable active kinase. Active ZmTTK1 controls transcriptional activation of genes in the anthocyanin biosynthesis pathway rerouting phenylalanine away from lignin biosynthesis. Therefore, we performed microarray analysis to understand how maize gene transcription in phenylpropanoid pathway is differentially changed after infection with Ustilago maydis SG200 (wild type) and SG200Dtin2 (anthocyanin-inducing effector mutant).
2014-01-28 | GSE48536 | GEO
Project description:Anthocyanin induction in plant is considered a general defense response against biotic and abiotic stresses. The infection by Ustilago maydis, the corn smut pathogen, is accompanied with anthocyanin induction in leaf tissue. We revealed that anthocyanin is intentionally induced by the virulence promoting secreted effector protein Tin2. Tin2 protein functions inside plant cells where it interacts with cytoplasmic maize protein kinase ZmTTK1. Tin2 masks an ubiquitin-proteasome degradation motif in ZmTTK1 leading to a more stable active kinase. Active ZmTTK1 controls transcriptional activation of genes in the anthocyanin biosynthesis pathway rerouting phenylalanine away from lignin biosynthesis. Therefore, we performed microarray analysis to understand how maize gene transcription in phenylpropanoid pathway is differentially changed after infection with Ustilago maydis SG200 (wild type) and SG200Dtin2 (anthocyanin-inducing effector mutant). We prepared three biological replicates for mock-inoculated maize (control), SG200-infected maize and SG200M-NM-^Ttin2-infected maize. For 1 sample, we harvested the leaves (1-3cm below injection hole) from 20 plants and pooled them. At 4 days post inoculation, total RNA was extracted.
2014-01-28 | E-GEOD-48536 | biostudies-arrayexpress
Project description:Zea mays transcriptome profiling of infected seedlings by the Ustilago maydis wildtype and the seedling specific effector mutant demonstrated the variation of gene expression in the mutant and the classes of genes that are absent in the mutant as compared to the wildtype U. maydis SG200 strain. Two dye competitive hybridizations were performed on Agilent Oligo arrays. Comparison were done 1) with mock and infected samples at 6dpi. 2) between the two 6dpi infected samples with wildtype and the secreted effector mutant
2015-03-09 | E-GEOD-63077 | biostudies-arrayexpress
Project description:The rep1 gene of the maize pathogen Ustilago maydis encodes a pre-pro-protein that is processed in the secretory pathway into 11 peptides. These so-called repellents form amphipathic amyloid fibrils at the surface of aerial hyphae. Strains in which the rep1 gene is inactivated (∆rep1 strain) are affected in aerial hyphae formation. This makes these strains instrumental to assess changes in global gene expression as a consequence of aerial growth. Microarray analysis revealed that only 31 genes in the ∆rep1 SG200 strain had a fold change in expression of >= 2. Twenty-two of these genes are up-regulated and half of them encode small secreted proteins (SSP’s) with unknown functions. Seven of the SSP genes and two other genes that are over-expressed in the ∆rep1 SG200 strain encode secreted cysteine-rich proteins (SCRP’s). Interestingly, most of the SCRP’s are predicted to form amyloids. The SCRP gene um00792 showed the highest up-regulation in the ∆rep1 strain. Using GFP as a reporter, it was shown that this gene is over-expressed in the layer of hyphae at the medium-air interface. Taken together, it is concluded that only minor changes occur in the expression profile when U. maydis forms aerial structures. Key words: aerial hypha, repellent, hydrophobin-like protein, Ustilago maydis, SSP, SCRP, fungal pathogenicity.
2011-05-01 | GSE21490 | GEO