Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Expression data of FB2 vs. FB2khd4Delta

ABSTRACT: RNA-binding proteins constitute key factors of the posttranscriptional machinery. These regulatory proteins recognise specific elements within target transcripts to promote e.g. maturation, translation or stability of mRNAs. In Ustilago maydis, evidence is accumulating that posttranscriptional processes are important to determine pathogenicity. Deletion of khd4, encoding a predicted RNA-binding protein with five K homology (KH) domains, causes aberrant cell morphology and reduced virulence. Here, we demonstrate that Khd4 recognises the sequence AUACCC in vivo via its tandem KH domains 3 and 4. This sequence functions most likely as regulatory RNA element in U. maydis, since it accumulates in 3â untranslated regions. Consistently, an independent transcriptional profiling approach revealed that the binding motif is significantly enriched in transcripts differentially regulated in khd4 strains. Since the vast majority of potential Khd4 target mRNAs exhibit increased expression in deletion mutants, Khd4 might promote mRNA instability. Mutants that fail to bind AUACCC resemble deletion mutants exhibiting altered cell morphology, disturbed filamentous growth and severely reduced virulence. Hence, RNA binding is essential for function of Khd4 stressing the importance of posttranscriptional control in regulating morphology and pathogenicity. keywords: gene deletion, RNA-binding protein, KH domain Strains FB2 (2 replicates, control) and FB2khd4Delta (2 individuals) were grown in minimal medium containing glucose and glutamine.

ORGANISM(S): Ustilago maydis

SUBMITTER: Michael FeldbrÃ¼gge

PROVIDER: E-GEOD-17956 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis.

Vollmeister Evelyn E Haag Carl C Zarnack Kathi K Baumann Sebastian S König Julian J Mannhaupt Gertrud G Feldbrügge Michael M

RNA (New York, N.Y.) 20091023 12

RNA-binding proteins constitute key factors of the post-transcriptional machinery. These regulatory proteins recognize specific elements within target transcripts to promote, for example, maturation, translation, or stability of mRNAs. In Ustilago maydis, evidence is accumulating that post-transcriptional processes are important to determine pathogenicity. Deletion of khd4, encoding a predicted RNA-binding protein with five K homology (KH) domains, causes aberrant cell morphology and reduced vir ...[more]

PMID: 19854870

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Project description:The fungus Ustilago maydis is a biotrophic pathogen of corn. In its genome we have identified an ortholog of YAP1 from Saccharomyces cerevisae which regulates the oxidative stress response in this organism. yap1 mutants of U. maydis displayed higher sensitivity to H2O2 than wild type cells and their virulence was significantly reduced. U. maydis yap1 could partially complement the H2O2 sensitivity of a yap1 deletion mutant of S. cerevisiae and a Yap1-GFP fusion protein showed nuclear localization after H2O2 treatment, suggesting that Yap1 in U. maydis functions as a redox sensor. Mutations in two cysteine residues prevented accumulation in the nucleus and the respective mutant strains showed the same virulence phenotype as Dyap1 mutants. DAB staining revealed an accumulation of H2O2 around yap1 mutant hyphae which was absent in wild type. Inhibition of the plant NADPH oxidase prevented this accumulation and restored virulence. During the infection Yap1 showed nuclear localization after penetration up to 2-3 days after infection. Through array analysis a large set of yap1 regulated genes were identified and these included two peroxidase genes. Deletion mutants of these genes were attenuated in virulence. These results suggest that U. maydis is using its yap1 controlled H2O2 detoxification system for coping with early plant defense responses. Keywords: Oxidative stress, yap1 dependent genes, Ustilago maydis Two independent overnight cultures of U. mayidis FB1 and FB1Dyap1 grown in CM-glucose (OD600 0.8) were diluted in 100 ml of the same medium (OD600 0.2) and growth at 28Â° C until an OD600 0.6. The cultures were divided and one half was supplemented with 5mM H2O2. After one hour of exposition to H2O2, cells were harvested by centrifugation and frozen in liquid nitrogen. RNA extraction, purification, cDNA generation, purification and labeling were performed according to standard protocols (Affymetrix). DNA array analysis was performed performed on two biological replicates each, using custom-designed Affymetrix chips (MPIUstilagoA). Data were analysed using a GeneArray Scanner (Agilent/Affymetrix) and the GeneChip Expression Analysis software (GCOS)

Project description:Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. Many of the genes coding for secreted protein effectors are arranged in gene clusters in the genome of the biotrophic plant pathogen Ustilago maydis. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. The generation and analysis strains carrying sub-deletions identified 9 genes significantly contributing to tumor formation after seedling infection. As the individual contributions of these genes to tumor formation were small, we studied the response of maize plants to the whole cluster mutant as well as to several individual mutants by array analysis. This revealed distinct plant responses, demonstrating that the respective effectors have discrete plant targets. We used the Affymetrix maize genome array to analyze the transcriptional responses of maize to cluster 19A mutants and individual sub-deletions for the cluster 19A genes tin1, tin3, tin4 and tin5. We found plant responses to the mutants were significantly different although the macroscopic phenotypes of the individual mutants were very similar. U. maydis infected parts of maize seedling leaves were dissected 4 days after inoculation with strain SG200∆19A, SG200∆tin1, SG200∆tin3, SG200∆tin4 and SG200∆tin5, respectively. We previously submitted data of maize leaves that were treated with the progenitor wild type strain SG200 as well as mock-infections under identical experimetal conditions (GEO: GSE10023). These data served as controls for this experiment.

Dataset Information

Expression data of FB2 vs. FB2khd4Delta

Publications

Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis.

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