The transcriptional profilling of the thermosensitive self-incompatible het-R het-V strain undergoing cell death by incompatibility
Ontology highlight
ABSTRACT:
ORGANISM(S): Podospora anserina
SUBMITTER: Frederique Bidard
PROVIDER: E-GEOD-21659 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:In the filamentous fungus Podospora anserina, cell death by incompatibility can be monitored using the conditional self-incompatible (SI) het-R het-V strain. SI strains are homokaryotic strains bearing incompatible het genes in all nuclei. The co-expression of these het genes triggers cell death in all the cells and hence in the entire mycelium. The het-R het-V SI strain, bearing the two incompatible het-R and het-V genes, proved particularly convenient as cell death triggering is thermosensitive (J. Labarère et al., 1973, C R Acad Sci Hebd Seances Acad Sci D, 276) and is induced by a simple shift in growth temperature (from 32°C to 26°C).The development of this cell death reaction has been recorded for 4 h after transfer to the restrictive temperature. A time course (T0h to T4h) of the transcriptomic response to the temperature shift has been explored in parallel within SI (het-R het-V) and wild type (compatible het-r hetV) s strains.
2013-01-01 | GSE21659 | GEO
Project description:Sexual reproduction in flowering plants involves intimate interactions between the growing pollen tube and the female reproductive structure. These interactions start immediately after pollen landing on the stigma and continue during the pollen tube journey through the style and the ovary. Thus, well before fertilization, genes in the gynoecium are affected by the growing pollen tubes. Genes activated at a distance in the ovary before pollen tubes arrival represent one class of such genes. Using a global transcriptomic approach, expression profiles obtained from compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations revealed that these pollinations are perceived differently from a distance in the ovary. As the pollen tubes grew along the style, more and more genes became specific for each pollination type, although even early on when no difference could be observed in pollen tube growth rates, each pollination type already displayed its specific signature. Wounding experiments as well as methyl jasmonate treatment were also conducted to determine if transmitting tissue cell death caused by pollen tube growth in the style could also activate gene expression at distance in the ovary. Our data suggest that pollen tube growth in the style is at least partially perceived as a wounding aggression, and that a SI pollination is more akin to a wound response than the other pollination type tested, suggesting similarities in the signaling pathways controlling pollen recognition and stress responses. More importantly, our transcriptomic analysis reveals a highly specific recognition of various pollination types that is relayed from a distance to the ovary ahead of fertilization. To determine on a more global scale if interorgan communication during pollen-pistil interactions is a widespread phenomenon and does not only involve few specialized genes, we used a 7.7K cDNA microarray comprising ~6500 ovule-derived unigenes in duplicata from Solanum chacoense, a self-incompatible wild potato species (Germain et al., 2005), to conduct gene expression analyses through cDNA microarray hybridizations. Profiles obtained from compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations as well as from wounding treatments were all analyzed using the same minimal expression level critera (p < 0.05, fold change ≥± 1.5). Four independent biological replicates were produced from each time points. Ovules were collected at 6, 24 and 48 hours after each treatment and used for RNA extraction and probe preparation . compatible (SC), incompatible (SI), semi-compatible (SeC) and interspecific (IS) pollinations as well as from wounding treatments mRNA preparations were individually hybridized against unpollinated ovule mRNAs . All data was substracted from the touch control. Althought Methanol treated ovules RNA were hybridized against unpollinated ovule mRNAs from plant in closed chamber. To estimate reproducibility and to produce control data for statistical analysis, a large number of unfertilized ovules were isolated and separated between seven independent control groups. RNA from randomly selected pairs of control was hybridized on six microarrays.
2010-05-26 | E-GEOD-21957 | biostudies-arrayexpress
Project description:Abstract BACKGROUND: Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat- mating types are determined by dissimilar allelic sequences. The mat- sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. METHODOLOGY/PRINCIPAL FINDINGS: The transcriptomic profiles of the mat+ and mat- strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1(-) and fpr1(-) mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat- strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. CONCLUSIONS/SIGNIFICANCE: This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating. With GPL10116 : 4 conditions each with four biological replicates :mat+, mat-, fpr1-, fmr1-; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5
2011-12-22 | E-GEOD-27297 | biostudies-arrayexpress
Project description:Abstract In Podospora anserina, the two zinc cluster proteins RSE2 and RSE3 are essential for the expression of the gene encoding the alternative oxidase (aox) when the mitochondrial electron transport chain is impaired. In parallel they activated the expression of gluconeogenic genes encoding phosphoenolpyruvate carboxykinase (pck) and fructose-1,6-biphosphatase (fbp). Orthologues of these transcription factors are present in a wide range of filamentous fungi and no other role than the regulation of these three genes has been evidenced so far. In order to better understand the function and the organisation of RSE2 and RSE3, we conducted a saturated genetic screen based on the constitutive expression of the aox gene. We identified 10 independent mutations in 9 positions in rse2 and 11 in 5 positions in rse3. Deletions were generated at some of these positions and the effects analyzed. This analysis suggests the presence of central regulatory domains and a C-ter activation domain in both proteins. Microarray analysis revealed 598 genes that were differentially expressed in the strains containing gain- or loss-of-function mutations in rse2 or rse3. It showed that in addition of aox, fbp and pck, RSE2 and RSE3 regulate the expression of genes encoding the alternative NADH dehydrogenase, a Zn2Cys6 transcription factor, a flavohemoglobin and various hydrolases. As a complement to expression data, a metabolome profiling approach revealed that both an rse2 gain-of-function mutation and growth on antimycin result in similar metabolic alterations in amino acids, fatty acids and M-NM-1-ketoglutarate pools. With GPL10116: 7 conditions each with four biological replicates: wt, rse2Y326D, rse3G642V, rse2Y326D-rse3G642V, M-NM-^Trse2, M-NM-^Trse3 and M-NM-^Trse2-M-NM-^Trse3; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5
2013-10-22 | E-GEOD-51360 | biostudies-arrayexpress
Project description:To gain insight into the targets of the PaMpk1 and PaMpk2 MAPK, we here determine the transcription profile of the mutants inactivated for PaMpk1, PaMpk2 and PaNox1 during vegetative growth at stages where they are required for proper development, in comparison with wild type. Microarrays representing 10556 coding sequences (CDS) predicted by the P. anserina genome project were used to estimate the transcription profiles (transcriptomes) during vegetative growth of three-day-old homokaryotic cultures of M-bM-^HM-^FPaMpk1, M-bM-^HM-^FPaMpk2 and the IDC343 PaNox1 mutants in comparison to wild type. Three zones corresponding to three developmental stages can be defined in such wild-type culture. From the growing edge the colony, the first five milimeters (zone 1) are constituted of hyphae lacking pigment and growing on the substrate. In this zone, very few hyphae are aerial and appressorium-like structures are not differentiated. In the second intermediate zone (zone 2), profuse aerial hyphae and appressorium-like structures are differentiated. This zone is about 7 mm wide and corresponds to the area where most perithecia are differentiated during sexual development of heterokaryotic mycelia. The zone that is most distal from the edge lack aerial hyphae (zone 3) accumulates a larger amount of pigment and differentiates few perithecia during sexual reproduction. It is about 1 cm wide. These three zones are easily visualized by the naked eye for sample recovery. The M-bM-^HM-^FPaMpk1, M-bM-^HM-^FPaMpk2 and the IDC343 PaNox1 mutants lack a clear zonation, since the three genes are involved in the signalling of stationary phase . Materials from these mutants were nonetheless recovered as three samples corresponding to the same zones, based mostly on the distance from the growing edge but also from subtle morphological differences. With GPL10116 : reference design, 4 strains (WT, M-bM-^HM-^FPaMpk1, M-bM-^HM-^FPaMpk2 and IDC343 PaNox1 with 3 growth conditions (zone1,2 and 3) each with four biological replicates, the common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5
2012-06-11 | E-GEOD-21331 | biostudies-arrayexpress
Project description:A genome wide microarray, covering the 10546 presently known and predicted CDS, has been constructed with the Agilent in-situ synthesized 60-mers technology. 1) A library of 10 oligonucleotides per CDS has been design by the manufacturer. 2) A computational step has been performed to determine 3' position, intron position and cross-hybridization rate of all probes. These data have been compiled to attribute a score to each probe and thus, to select a first set of 4 oligonucleotides per CDS. 3) Microarray v.2 (GPL10115), manufactured with this design, have been used for a selection procedure based on the use of transcriptomic experimental data generated with diverse culture conditions. To maximize the number of expressed CDS, experimental data were generated with a large range of growth conditions covering crucial physiological changes from key steps of vegetative growth and sexual development.For each condition, four biological replicates were done to increase the statistical power of the analysis. An oligonucleotide scoring has been settled to select the best oligonucleotide per CDS. The final array design, Microarray v.3 (GPL10116), contained 10,539 probes for nuclear CDS. The array was enriched with 17 mitochondrial CDS probes that did not undergo the experimental screening. Each probe was replicated four times on each 44K array to improve the statistical significance of results. Before using in industrious transcriptomic experiment, ultimate qualification steps have been carried out. First, DNA extracted from the/ S/ and /s /strains was hybridized with the final design Microarray v.III. The apha_ORF and /het/ genes were identified as polymorphic between /s/ and /S/ strains (|FC|>2; a/ =/0.001) confirming previous genetic and molecular analyses (Turcq B etal.,1990*,* /Current genetics, /Sellem et al., 1990, Mol. Gen. Genet.). In second qualification step, a self-to-self hybridization experiment, replicated three times, has been /per/formed with a commonreference: 89.3% of the probes displayed a signal-to-standard-deviation ratio >3. The final microarray design is referenced as AMADID 018343. Microarray slides are available to the research community from Agilent. We developed oligonucleotide microarrays for the filamentous fungus Podospora anserina as part of the ANR program project grant ANR-05-BLAN-0385 (project SexDevMycol), coordinated by R. Debuchy. This project was aimed to analyze the sexual development of /P. anserina/ with a variety of approaches, including transcriptomic profiling. Different versions of microarrays were tested on mycelium and sexual development time courses, to evaluate their perfomance in comparing transcriptomic profiles of vegetative vs sexual stages, and in analyzing transcriptomic profiles evolution during sexual development. Complete analyses were performed with the microarray final version (v.III) and several manuscripts dealing with these topics are in preparation. The s (small s) and S (big S) strains of Podospora anserina are different geographical isolates of the same species. Both strains can cross and have identical ITS (accession #: AY278557 and GU391422) confirming that they belong to the same species. The S strain has been completely sequenced (Espagne et al., Genome Biology, 2008, 9, R77 ) and its genome is currently at the finishing step (P. Silar and P. Wincker, unpublished results). The genome of the s strain is not sequenced, and only a few genes are known. The major known difference is at the level of the s locus controling vegetative incompatibility (Turcq et al., Current genetics 1990, 17:297-303). PART1 (with GPL10115): reference design, 5 conditions each with four biological replicates : M24h, M48h, M96h, C24h, C48h; common reference is a pool of four conditions M48h, M96h, C48h and C96h ; Conditions are labelled in Cy3 and the common reference in Cy5 PART2 (with GPL10116): DNA hybridization with a direct design, wt s versus wt S, dye swap (four technical replicates); RNA Homotypic hybridization with the common reference sample (three technical replicates)
2010-06-30 | E-GEOD-20734 | biostudies-arrayexpress
Project description:A comparative proteomic analysis of grapevine leaves from the resistant genotype V. davidii ‘LiuBa-8’ (LB) and susceptible genotype V. vinifera ‘Pinot Noir’ (PN) at 12 hpi was conducted to understand the complex relationship between grapevine and P. viticola and the molecular mechanisms between difference resistant vitis genotypes at the early stage of infection. A total of 444 and 349 differentially expressed proteins (DEPs) were identified in LB and PN respectively at 12 hpi by iTRAQ. MapMan analysis showed that the majority of these DEPs were related to photosynthesis, metabolism, stress and redox. More up-expressed DEPs involved in photosynthesis and less down-expressed DEPs involved in metabolism contribute to the resistance in LB. PR10.2, PR10.3, HSF70.2 and HSP90.6 are proposed to be key proteins in both compatible and incompatible interactions. Accumulation H2O2 established the ROS signaling in incompatible interaction and APXs, GSTs maybe associated with the resistance of grapevine against downy mildew. Moreover, we verified four proteins to ensure the accuracy of proteome data using PRM. Overall, these data provide new insights into molecular events and provide valuable candidate proteins that could be used to illuminate molecular mechanisms underlying the incompatible and compatible interaction in early stage and eventually to be exploited to develop new protection strategy against downy mildew in grapevine.
2021-09-09 | PXD018868 | Pride
Project description:To investigate the protein expression changes at the synapse induced by Eef2 reduction, we performed (LCMS)/MS-based proteomic analysis in crude synaptosome preparations from the PFC of WT and Eef2 HET mice.
2022-08-15 | PXD034864 | Pride
Project description:We report the heart RNA-sequencing of control animals (129S6 genetic background, wild type). Animal models comprise of Titin PEVK homozygous deletion of exons 219-225 (PEVK-KO), RBM20 heterozygous deletion of exons 6-7 (RBM20-HET), and double deletion (PEVK-KOxRBM20-HET). RNA from left ventricular tissue was isolated using TRIzol followed by a clean-up with the QIAGEN RNA micro kit, cDNA libraries were generated using the Illumina TruSeq Stranded mRNA Sample Prep Kit 2x101 paired-end sequenced on HiSeq2000 (WT, RBM20-HET) or HiSeq4000 (PEVK-KOxRBM20-HET). Trimming and quality clipping was performed with Flexbar v. 3.03. The remaining reads greater than 18bp were mapped to the murine genome (assembly EnsEMBL 84) with the splice-aware STAR aligner v. 2.5.1b. Transcriptome analyses on differential gene and isoform abundance were carried out with cuffdiff 20 v. 2.2.1.
2023-11-30 | E-MTAB-11124 | biostudies-arrayexpress
Project description:The purpose of this study is to investigate the role of SIRT1 in high-fat diet-induced liver steatosis and insulin resistance. SIRT1 is a nuclear enzyme that could remove an acetyl-group from target proteins by using NAD as co-substrate. Homologs of this protein in yeast and the roundworm C. elegans are able to delay the aging process in response to nutrients. However, the molecular mechanism by which SIRT1 sense the environment to mediate this response are poorly understood. We have shown that when chronically fed with a 40%-fat diet, SIRT1 heterozygous animals gain significantly more weight compared to wild type littermates. They are also hyperinsulimia, more insulin-resistant, and accumulate more lipids in liver. Interestingly, these animals also show signs of premature aging, such as an early appearance of gray fur, defective motor activity, and decreased fertility. In this microarray study, we analyzed the gene expression profiles in the liver of WT low-fat diet, Het low-fat diet, WT high-fat diet, and Het high-fat diet using Agilent Whole Genome Mouse 4x44 multiplex format oligo arrays following the Agilent-1-color microarray-based gene expression analysis protocol. This microarray analysis concluded that SIRT1 Het mice reponsed to the high-fat diet differently from the WT control mice. Liver total RNAs from SIRT1 WT and Het mice that were fed with either a low-fat diet or a high-fat diet for 34 weeks were used for a microarray gene expression study. Three biological replicates for each group were used.
2012-07-31 | E-GEOD-39778 | biostudies-arrayexpress