RNAseq of Ustilago maydis strain AB31 and AB31_delta_Num1
Ontology highlight
ABSTRACT:
ORGANISM(S): Ustilago maydis
SUBMITTER: Florian Finkernagel
PROVIDER: E-MTAB-1300 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
The SPF27 homologue Num1 connects splicing and kinesin 1-dependent cytoplasmic trafficking in Ustilago maydis.
Kellner Nikola N Heimel Kai K Obhof Theresa T Finkernagel Florian F Kämper Jörg J
PLoS genetics 20140102 1
The conserved NineTeen protein complex (NTC) is an integral subunit of the spliceosome and required for intron removal during pre-mRNA splicing. The complex associates with the spliceosome and participates in the regulation of conformational changes of core spliceosomal components, stabilizing RNA-RNA- as well as RNA-protein interactions. In addition, the NTC is involved in cell cycle checkpoint control, response to DNA damage, as well as formation and export of mRNP-particles. We have identifie ...[more]
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2011-07-05 | E-GEOD-30382 | biostudies-arrayexpress
Project description:Hxt1 is a high affinity hexose transporter important for virulence of the phytopathogenic basidiomycete Ustilago maydis on its host plant maize. Hxt1 shows the highest similarities to the glucose sensors Rgt2 and Snf3 from S. cereviciae (42% and 39% identity on amino acid level, respectively). In these sensors, the substitution of a highly conserved arginine to lysine leads to a constitutive active signal, resulting in expression of several glucose induced genes. Introduction of an analogous mutation in Hxt1 leads to loss of transport activity in the resulting Hxt1(R164K) protein. Expression of Hxt1(R164K) in hxt1 deletion strains results in a completely avirulent phenotype. Pathogenic developement of M-bM-^HM-^Fhxt1 hxt1(R164K) strains is blocked immediately after plant penetration. Expression analysis of M-bM-^HM-^Fhxt1 hxt1(R164K) cells 24 hours post inoculation revealed downregulation of a set of genes involved in carbohydrate metabolism indicating a role of Hxt1 in carbohydrate signaling during initiation of the pathogenic stage. To analyze expression changes of SG200 and SG200M-bM-^HM-^Fhxt1 and SG200M-bM-^HM-^Fhxt1 hxt1(R164K) cells were harvested from the surface of maize leaves 24 hour post inoculation. For each strain three independent replicates were conducted.
2014-09-04 | E-GEOD-61069 | biostudies-arrayexpress
Project description:Infection-related development of phytopathogenic fungi is initiated by sensing and responding to plant surface cues. This response results in the formation of specialized infection structures, so-called appressoria. To unravel the program inducing appressoria in the biotrophic smut fungus Ustilago maydis, we exposed cells to a hydrophobic surface and the cutin monomer 16-hydroxy hexadecanoic acid. Genome-wide transcriptional profiling under these appressorium-inducing in vitro conditions revealed dramatic transcriptional changes in almost 20% of the genes. Comparisons with the U. maydis sho1 msb2 double mutant, lacking two putative sensors for plant surface cues, revealed that these plasma membrane receptors regulate a small subset of the surface cue-induced genes. These genes comprised mainly secreted proteins including plant cell wall degrading enzymes that facilitate plant penetration and secreted effectors that are essential virulence factors, with functions after penetration. Our data also demonstrate specific effects on two transcription factors that redirect the transcriptional regulatory network towards appressorium formation and plant penetration. Thus, plant surface cues prime U. maydis for biotrophic development. Solopathogenic Ustilago maydis strain AM1 and its derivate AM1Δsho1Δmsb2 were grown to mid-log phase in YEPSL medium and resuspended in 2% YEPSL plus/minus 16-hydroxy hexadecanoic acid (HDA). The cell suspensions were sprayed on hydrophobic surface (Parafilm) and incubated for 12 h. As control, cells were sprayed on hydrophilic glass surface and incubated for 2 h. After RNA extraction Affymetrix microarrays were performed.
2014-07-23 | E-GEOD-53947 | biostudies-arrayexpress
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Project description:Elicidate the changes of the transcriptional program response of U. maydis WT strain (a2b2) when transfered from neutrality to acidic or alkaline medium The mutants strains CL211 and GP25 used as controls as well as the WT strain are described in MartÃnez-Espinoza et al., 1997; 2004;González-Prieto et al., 2014 and Banuett & Herskowitz, 1989 respectively. High density-one color arrays from Nimblegen were used according to a design from Scott Gold from University of Georgia. The design has five different oligonucleotides of 60 bp in lenght in duplicate, representing each one of the 6883 gene of the U. maydis genome.
2016-02-23 | E-GEOD-75053 | biostudies-arrayexpress
Project description:Goals: characterization of the transcription factor Ros1 in Ustilago maydis Methods: generation of deletion mutants, microscopic observations, ectopic expression of ros1, identification of Ros1 regulated genes by RNAseq and ChIP sequencing Results: Ros1 is not involved in plant colonization but is essential to trigger sporogenesis during late stages of infection. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP seq analyses revealed that Ros1 affects the expression of about 30 % of all U. maydis genes with 40% being direct targets. Cell wall remodeling and plasma membrane modifications are among the processes affected by Ros1 dependent regulation. Interestingly a large number of b-dependent genes including transcription factors and effector genes involved in biotrophy establishment were downregulated by Ros1 while a subset of novel â??late effectorsâ?? were upregulated. Taken together our results indicate that Ros1 is a master regulator of sporogenesis in U. maydis and that the switch to sporogenesis is accompanied by the differential regulation of 75% of the effector genes. 4 samples were analyzed in triplicate. The first two samples correspond to input and output DNA obtained from ChIP carried out on plant material infected with U. maydis strains expressing Ros1 with an HA tag. The other two other samples correspond to input and output DNA from ChIP carried out on plant material infected with U. maydis strains expressing Ros1 without a tag (control samples).
2016-06-24 | E-GEOD-76230 | biostudies-arrayexpress
Project description:Goals: characterization of the transcription factor Ros1 in Ustilago maydis Methods: generation of deletion mutants, microscopic observations, ectopic expression of ros1, identification of Ros1 regulated genes by RNAseq and ChIP sequencing Results: Ros1 is not involved in plant colonization but is essential to trigger sporogenesis during late stages of infection. Premature expression of ros1 revealed that Ros1 counteracts the b-dependent filamentation program and induces morphological alterations resembling the early steps of sporogenesis. Transcriptional profiling and ChIP seq analyses revealed that Ros1 affects the expression of about 30 % of all U. maydis genes with 40% being direct targets. Cell wall remodeling and plasma membrane modifications are among the processes affected by Ros1 dependent regulation. Interestingly a large number of b-dependent genes including transcription factors and effector genes involved in biotrophy establishment were downregulated by Ros1 while a subset of novel â??late effectorsâ?? were upregulated. Taken together our results indicate that Ros1 is a master regulator of sporogenesis in U. maydis and that the switch to sporogenesis is accompanied by the differential regulation of 75% of the effector genes. Two samples corresponding to plant material infected with either U. maydis wild type strains FB1 x FB2 or the ros1 deletion strains FB1Dros1 x FB2Dros1 were analyzed in triplicate.
2016-06-24 | E-GEOD-76229 | biostudies-arrayexpress
Project description:Ustilago maydis is a plant-pathogenic fungus that establishes a biotrophic relationship with its host Zea mays. The biotrophic interaction is initiated upon host penetration, and involves expansion of the host plasma membrane around hyphae, which is thought to facilitate the exchange of nutrients and virulence factors. Transcriptional regulators involved in the establishment of an infectious dikaryon and penetration into the host have been identified, however, regulators involved in the post-penetration stages remained to be elucidated. In the study we report the identification of an Ustilago maydis forkhead transcription factor, Fox1, which is exclusively expressed during biotrophic development. Deletion of fox1 results in reduced virulence and impaired tumour development in planta. Microarray analyses of Δfox1-infected plant tissue identified Fox1 as a transcriptional activator, involved in the expression of secreted effectors required for virulence. Maize plants were infected with a mixture of either FB1 and FB2 (wild-type), or FB1∆fox1 and FB2∆fox1 crossings, to measure the impact of fox1 on pathogenic development. Early Golden Bantam maize plants were grown in a phytochamber in a 15h/9h light-dark cycle; light period started/ended with 1h ramping of light intensity. Maize plants were kept at 28°C (light) and 20° (dark). Plantlets were individually sown in pots with potting soil (Fruhstorfer Pikiererde) and infected 7 days after sowing, 1 h before end of the light period. Infected leaf tumor material from at least 10 plants was collected 5 days post infection, 1 h before the end of the light period and directly frozen in liquid nitrogen for RNA-extraction. RNA samples were extracted from infected leaf tissue 5 days after infection.
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2014-02-04 | E-GEOD-54659 | 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). 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