{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Gunther Doehlemann"],"organism":["Zea mays"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-GEOD-48406"],"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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Treatment - U. maydis strain SG200 (Nature 444:97-101) was grown in liquid culture overnight to an OD600 of 1.0, harvested by centrifugation, and resuspended in water to an OD600 of 3.0; compatible strains were mixed in equal amounts immediately before infection; 0.2 ml of cell suspension mixes were injected into the leaf whorl of 6–7-day-old corn plants (as described in Mol Microbiology 42:1047-1063). Plants were infected 7 days after sowing 1 h before end of the light period with the exception of the 12 hpi samples were plants were infected during the beginning of the light period.","Scaning - Microarrays were scanned on an Affymetrix GSC3000.","Hybridization - Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using protocol Midi_Euk2V3.","Sample Treatment - Seedlings were inoculated 7 days after sowing with the respective U. maydis strains, resulting in an infection of the third seedling leaf. Samples were taken 4 days after fungal infection.","Nucleic Acid Extraction - For RNA isolation, material from 30 plants was pooled and subsequently ground in liquid nitrogen by mortar and pestle. RNA was extracted from the powder with Trizol (Invitrogen) and purified using the Qiagen RNeasy kit, according to the manufacturer’s instructions, respectively.","Scaning - GeneChips were scanned on a Affymetrix GSC3000G scanner","Growth Protocol - Maize plants of the cultivar Early Golden Bantam were grown in a phyto chamber in a 15 h / 9 h light-dark cycle; light period started with a continuous increase from 0% to 100% light for 1h, and ended 13h later with a continuous decrease from 100% to 0% light for 1 h. Temperature was 28C and 20C, relative humidity 40% and 60% during light and dark periods, respectively, with a 1 h ramping for both values. Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) to avoid shading of the plants.","Nucleic Acid Extraction - Trizol extraction of total RNA was performed according to the manufacturer's instructions.","Labeling - Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).","Hybridization - Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Maize Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 (Expression Analysis Technical Manual, 2001, Affymetrix)","Growth Protocol - Maize plants (Early Golden Bantam) were grown in a phyto chamber in a 15/9 hour light/dark cycle. Temperature was 28C and 20C, relative humidity 40% and 60% during light and dark periods, respectively, with 1 hour ramping for both parameters."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Data Transformation - Data were analyzed with Microarray Suite version 5.1 (MAS 5.1) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300. ID_REF =  VALUE = MAS 5.1 signal intensity ABS_CALL =  DETECTION P-VALUE =","Data Transformation - Date were analyzed with the GeneChip operating software (GCOS) 1.4 to generate CEL files. ID_REF =  VALUE = Signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE ="],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"pubmed_abstract":["In the genome of the biotrophic plant pathogen Ustilago maydis, many of the genes coding for secreted protein effectors modulating virulence are arranged in gene clusters. The vast majority of these genes encode novel proteins whose expression is coupled to plant colonization. The largest of these gene clusters, cluster 19A, encodes 24 secreted effectors. Deletion of the entire cluster results in severe attenuation of virulence. Here we present the functional analysis of this genomic region. We show that a 19A deletion mutant behaves like an endophyte, i.e. is still able to colonize plants and complete the infection cycle. However, tumors, the most conspicuous symptoms of maize smut disease, are only rarely formed and fungal biomass in infected tissue is significantly reduced. The generation and analysis of strains carrying sub-deletions identified several genes significantly contributing to tumor formation after seedling infection. Another of the effectors could be linked specifically to anthocyanin induction in the infected tissue. 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 propose that the analysis of plant responses to effector mutant strains that lack a strong virulence phenotype may be a general way to visualize differences in effector function."],"study_type":["transcription profiling by array"],"species":["Zea mays"],"pubmed_title":["Characterization of the largest effector gene cluster of Ustilago maydis"],"pubmed_authors":["Shigeyuki Tanaka","Gunther Doehlemann","Thomas Brefort","Nina Neidig","Brefort T, Tanaka S, Neidig N, Doehlemann G, Vincon V, Kahmann R","Regine Kahmann"],"additional_accession":[]},"is_claimable":false,"name":"Maize gene expression during infection with the Ustilago maydis mutant for cluster 19A and subdeletions for individual genes of cluster 19A","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.","dates":{"release":"2014-09-01T00:00:00Z","modification":"2023-08-31T05:09:09.03Z","creation":"2022-03-04T17:53:08.808Z"},"accession":"E-GEOD-48406","cross_references":{"GEO":["GSE48406"],"pubmed":["24992561"],"EFO":["EFO_0002768"],"doi":["10.1371/journal.ppat.1003866"]}}