Differential gene expression of Appresorium vs Vegetative mycelium of Magnaporthe using oligoarray
Ontology highlight
ABSTRACT:
ORGANISM(S): Pyricularia grisea
PROVIDER: GSE5518 | GEO | 2006/08/18
SECONDARY ACCESSION(S): PRJNA96169
REPOSITORIES: GEO
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Project description:The identification of genes regulated by the transcription factor Bip1 during appressorial development. The rice blast fungus Magnaporthe grisea develops melanized appressoria with high turgor pressure that inject the fungus into epidermal host cells. A screen for M. grisea non-pathogenic mutants recovered mutant M763 with reduced penetration efficiency and infectious growth. Complementation analysis identified a gene inactivated in M763 that encodes a novel basic leucine zipper (bZIP) transcription factor named Bip1 (B-ZIP Involved in Pathogenesis1). Deletion of Bip1 by targeted replacement generated non-pathogenic mutants that are unable to infect rice or barley. These mutants develop melanized appressoria that are unable to penetrate intact or wounded host leaves. Bip1 mRNA was detected in fungal spores, appressoria and infected leaves but not in mycelia, while a BIP1:GFP fusion was detected only in nuclei of mature appressoria. Genome wide transcriptome analysis identified 44 genes down regulated in Δbip1:hph appressoria. Most of these genes (77%) are specifically expressed in appressoria and encode enzymes involved in secondary metabolism (11), secreted proteins and enzymes (18) and G-Protein Coupled Receptors (GPCRs) (5). Promoters of BIP1 down-regulated genes share a similar GCN4/bZIP DNA binding motif (TGACTC). Gel shift assays showed that the motifs from 6 of the 7 promoters tested bind to recombinant BIP1 in vitro, including MGG_08381.5 from the ACE1 locus. Mutation of BIP1 binding sites in the MGG_08381.5 promoter significantly reduced its appressorium specific expression. Molecular and biochemical studies confirmed that BIP1 controls the expression of a distinct set of M. grisea genes in the appressorium, revealing a novel regulatory network involved in early stages of fungal infection that activates a diverse gene expression program resulting in a “shock and awe” impact on the plant host.
2018-01-05 | GSE18823 | GEO
Project description:OsMKK4 is a rice MAPKK and immediately activated by treatment with chitin elicitor, a fungal MAMP. OsMKK4 phosphrylate and activate OsMPK6. We compared gene expression in osmpk6 and osmpk6 complemented cells expressing active OsMKK4 using rice 44K oligoarray.
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Project description:OsMKK4 is a rice MAPKK and immediately activated by treatment with chitin elicitor, a fungal MAMP. OsMKK4DD is a constitutively active mutants of OsMKK4. We identified OsMKK4 regulated genes using a conditional gain-of-function transgenic system and rice 44K oligoarray.
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Project description:SAGE and MPSS libraries were produced from the same RNA sample extracted from an activated CD4+ T cell clone in order to compare the ability of these techniques to indentify the full range of genes expressed in a single cell type. Keywords: Technical comparison of tag-based technologies SAGE and MPSS
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Project description:The hemibiotrophic fungus Magnaporthe oryzae produces specialized biotrophic invasive hyphae (IH) that alter membrane structure and defense responses in invaded rice cells. IH successively invade live neighbor cells, apparently through plasmodesmata. Understanding fungal and rice genes that contribute to biotrophic invasion has been a challenge because so few plant cells have encountered IH at the earliest infection stages. Using a rice sheath inoculation method, we successfully enriched for infected tissue RNA that contained ~20% fungal RNA at a point when most IH were still growing in first-invaded rice cells. The RNAs were analyzed using the whole-genome M. oryzae oligoarray and a rice oligoarray. Rice genes that were induced >50-fold during infection were enriched for genes involved in transferring information from sensors to cellular responses. Fungal genes that were induced >50-fold in IH included the PWL2 avirulence gene and genes encoding hypothetical secreted proteins. The IH-specific secreted proteins are candidate effectors, proteins that the fungus secretes into live host cells to control cellular processes. Gene knock-out analyses of three putative effector genes failed to show major effects on pathogenicity. Details of the blast interaction transcriptome will provide insights on the mechanisms of biotrophic plant disease. Keywords: Disease state analysis
2009-04-08 | GSE8518 | GEO
Project description:The hemibiotrophic fungus Magnaporthe oryzae produces specialized biotrophic invasive hyphae (IH) that alter membrane structure and defense responses in invaded rice cells. IH successively invade live neighbor cells, apparently through plasmodesmata. Understanding fungal and rice genes that contribute to biotrophic invasion has been a challenge because so few plant cells have encountered IH at the earliest infection stages. Using a rice sheath inoculation method, we successfully enriched for infected tissue RNA that contained ~20% fungal RNA at a point when most IH were still growing in first-invaded rice cells. The RNAs were analyzed using the whole-genome M. oryzae oligoarray and a rice oligoarray. Rice genes that were induced >50-fold during infection were enriched for genes involved in transferring information from sensors to cellular responses. Fungal genes that were induced >50-fold in IH included the PWL2 avirulence gene and genes encoding hypothetical secreted proteins. The IH-specific secreted proteins are candidate effectors, proteins that the fungus secretes into live host cells to control cellular processes. Gene knock-out analyses of three putative effector genes failed to show major effects on pathogenicity. Details of the blast interaction transcriptome will provide insights on the mechanisms of biotrophic plant disease. Keywords: Disease state analysis
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Project description:Oligoarray expression profiling was carried out in poplar leaves upon infection with rust in order to identify genes expressed during tree defense response. For this purpose, we inoculated detached leaves of the interamerican hybrid poplar Populus trichocarpa x Populus deltoides 'Beaupré' grown in greenhouse either with spores of avirulent strain 93ID6 (incompatible interaction I48) or spores of virulent strain 98AG31 (compatible interaction C48) of the pathogenic rust fungus Melampsora larici-populina. Besides, we mock-inoculated 'Beaupré' leaves with water (control condition, T48). Detached leaves were maintained in vitro in controled conditions to allow fungal infection and colonization of plant tissue. Leaves were sampled 48 hours post-inoculation after that the fungus attempt to penetrate plant cells in mesophyll. Keywords: Plant tissue infection, Plant defense response, Oligonucleotide array
2007-03-15 | GSE7098 | GEO
Project description:This series examines differential gene expression during germination and appressorium formation by the rice blast fungus Magnaporthe grisea. Conidia were germinated on either the hydrophobic (inductive) or hydrophilic (non-inductive) side of GelBond. RNA was extracted from conidia and following incubation for 7 and 12 hours. RNA from two biological replications of each treatment was pooled in equal amounts and labeled with both cy3 and cy5 dyes using the Agilent Technologies Low Input Linear Amplification Kit. Hybridizations were performed on Agilent Technologies whole genome oligo rice blast arrays (product G4137A) using manufacturer prescribed protocols and reagents in an interlaced loop design in which each treatment was paired with every other. This series contains a total of 10 hybridizations; each treatment was used in 4 hybridizations (2 with cy3 and 2 cy5). Spot fluorescence was normalized using Lowess within and between microarray slides in Bioconductor and gene expression profiles analyzed in GeneSpring. Keywords: other
2010-06-05 | E-GEOD-1945 | biostudies-arrayexpress
Project description:Identification of all expressed transcripts in a sequenced genome is essential both for genome analysis and for realization of the goals of systems biology. We used the transcriptional profiling technologies like ‘massively parallel signature sequencing (MPSS)’ and ‘Sequencing by Synthesis’ (SBS) to develop a comprehensive expression atlas of rice (Oryza sativa cv Nipponbare). Illumina’s SBS technology can generate large amounts of sequence data in a short time at low cost compared to traditional Sanger sequencing based methods. Using the MPSS technology, we previously analyzed the transcriptomes of 72 rice tissues. To validate the sequencing results from MPSS technology, we employed SBS technology and constructed SBS libraries from 32 rice tissues (47 libraries including replications). For SBS library construction, we used the same mRNA samples and same restriction enzyme (DpnII) that were used for the construction of the MPSS libraries. These libraries include six abiotic-stress libraries, eight pathogen-infected libraries, five insect-damaged libraries, three developing seed libraries, and 10 untreated rice tissue libraries. This study was carried out with the following objectives; a) Identification and quantification of expressed genes in rice at all developmental stages of plant growth, response to biotic and abiotic stresses, and developing seeds; b) Compare SBS signatures with rice genomic sequence to identify novel transcripts; c) To validate the transcriptional data obtained through MPSS technology; and To create query and analysis tools to facilitate public use of and access to rice MPSS and SBS data and to display abundance and chromosomal locations of rice MPSS and SBS signatures. The SBS data will be available at http://mpss.udel.edu/rice_sbs/.
2011-06-22 | GSE25596 | GEO
Project description:Germination and appressorium formation in Magnaporthe grisea
| PRJNA90443 | ENA