Project description:Arabidopsis thaliana (Col-0) plants were treated with beta-aminobutyric acid (BABA), and gene expression differences to control plants were monitored after infection with Pseudomonas syringae pv tomato DC3000 (Pst DC3000). Keywords: transcript profiling, response to BABA-induced priming and infection 2 independent replicates for each condition were analyzed by two color co-hybridizations. Leaf RNA from Pseudomonas-infected control plants (Cy3-labeled cDNA) cohybridized with leaf RNA from Pseudomonas-infected BABA-pretreated plants (Cy5-labeled cDNA). Samples were collected 22 hours after bacterial inoculation. BABA pretreatment was performed two days before bacterial inoculation.
Project description:Arabidopsis thaliana (Col-0) plants were treated with BABA and gene expression differences to control plants were monitored after dip-inoculation with Pseudomonas syringae pv tomato DC3000. Keywords: transcript profiling, response to BABA-induced priming and infection Overall design: 3 independant replicates were analyzed by two color co-hybridizations. Leaf RNA from Pseudomonas infected control plants (Cy3 labeled cDNA) was cohybridized with leaf RNA from Pseudomonas infected BABA pretreated plants (Cy5 labeled cDNA). Samples were collected 22 hours after bacterial inoculation. BABA pretreatment was performed two days before bacterial inoculation. To assess the effect of BABA alone on gene expression, leaf RNA from BABA treated plants (Cy5 labeled cDNA) was cohybridized with leaf RNA (Cy3 labeled cDNA) from water treated plants.
Project description:Plant immune response is a complex process involving both transcriptional and posttranscriptional regulation of gene expression. Here, we identify an Arabidopsis long-noncoding (lnc) RNA, designated elf18-induced long noncoding RNA 1 (ELENA1), as a factor enhancing resistance against Pseudomonas syringe pv. tomato DC3000. ELENA1 knock-down plants show a decreased expression of PR1 and the plants are susceptible to pathogens. By contrast, plants over-expressing ELENA1 show elevated Pathogenesis-Related gene 1 (PR1) expression after elf18 treatment and display pathogen resistance phenotype. RNA-seq analysis of ELENA1 overexpressing plants after elf18 treatment confirms increased expression of defense-related genes compared to WT. ELENA1 directly interacts with Mediator subunit 19a (MED19a) and affects enrichment of MED19a on PR1 promoter. These results show that ELENA1 is a novel lncRNA that regulates PR1 expression through MED19a. Our findings uncover an additional layer of complexity implicating lncRNA in the transcriptional regulation of plant innate immunity. Overall design: To investigate the role of ELENA1 in regulating immune response, we performed strand-specific RNA-seq (ssRNA-seq) on WT and ELENA1 OX plants grown under normal (0 h) and elf18-treated conditions (1 h, 6 h and 12 h). For each condition we used three biological replicates.
Project description:Microarray experiments to compare gene expression profiles of ate1 ate2 double-mutant plants and the wild type at different developmental stages and after the infiltration with Pseudomonas syringae strain Pst AvrRpm1. Overall design: Global gene expression in ate1 ate2 double mutant seedlings was compared to that in wild-type seedlings using Agilent whole-genome microarrays. In addition, the response of both ate1 ate2 mutant and wild-type plants to infection with Pseudomonas syringae strain Pst AvrRpm1 was tested at different time-points after infiltration.
Project description:We investigated the relationships of the two immune-regulatory plant metabolites salicylic acid (SA) and pipecolic acid (Pip) in the establishment of plant systemic acquired resistance (SAR) in Arabidopsis thaliana induced by the bacterial pathogen Pseudomonas syringae. To characterize the transcriptional SAR response, we used wild-type Col-0 plants, SA-deficient sid2 plants and Pip-deficient ald1 plants and performed RNA-sequencing analyses (Bernsdorff et al., Plant Cell, 2016). SAR establishment in the wild-type is characterized by a strong transcriptional response systemically induced in the foliage that prepares plants for future pathogen attack by pre-activating multiple stages of defense signaling. Whereas systemic Pip elevations are indispensable for SAR and necessary for virtually the whole transcriptional SAR response, a moderate but significant SA-independent component of SAR activation and SAR gene expression is revealed. Arabidopsis thaliana plants were grown individually in pots containing a mixture of soil, vermiculite and sand (8:1:1) in a controlled cultivation chamber with a 10-h day (9 AM to 7 PM; photon flux density 100 mol m-2 s-1) / 14-h night cycle and a relative humidity of 70 %. Day and night temperatures were set to 21C and 18C, respectively. Experiments were performed with 5- to 6-week-old, naive plants exhibiting a uniform appearance. To activate SAR, plants were infiltrated between 10 AM and 12 AM into three lower (1) leaves with suspensions of the bacterial pathogen Pseudomonas syringae pv. maculicola (OD600 = 0.005). Infiltration with 10 mM MgCl2 served as the mock-control treatment. Upper (2) leaves were harvested 48 h after the primary treatment for the determination of systemic gene expression by RNA-seq analyses. Three biologically independent, replicate SAR induction experiments were performed with Col-0 and sid2 plants (experimental set 1), and three other biologically independent experiments with Col-0 and ald1 plants (experimental set 2). In each SAR experiment, at least 6 upper (2) leaves from 6 different plants pre-treated in 1 leaves with Psm (MgCl2) were pooled for one biological Psm- (mock-control) replicate. In this way, 3 biologically independent, replicate samples per treatment and plant genotype were obtained within each SAR set.
Project description:Pseudomonas aeruginosa is an opportunistic human pathogen, infecting immuno-compromised patients and causing persistent respiratory infections in people affected from cystic fibrosis. Pseudomonas strain Pseudomonas aeruginosa PA14 shows higher virulence than Pseudomonas aeruginosa PAO1 in a wide range of hosts including insects, nematodes and plants but the precise cause of this difference is not fully understood. Little is known about the host response upon infection with Pseudomonas and whether or not transcription is being affected as a host defense mechanism or altered in the benefit of the pathogen. In this context the social amoeba Dictyostelium discoideum has been described as a suitable host to study virulence of Pseudomonas and other opportunistic pathogens.
Project description:<p>Gene expression is a biological process regulated at different molecular levels, including chromatin accessibility, transcription, and RNA maturation and transport. In addition, these regulatory mechanisms have strong links with cellular metabolism. Here we present a multi-omics dataset that captures different aspects of this multi-layered process in yeast. We obtained RNA-seq, metabolomics, and H4K12Ac ChIP-seq data for wild-type and mip6delta strains during a heat-shock time course. Mip6 is an RNA-binding protein that contributes to RNA export during environmental stress and is informative of the contribution of post-transcriptional regulation to control cellular adaptations to environmental changes. The experiment was performed in quadruplicate, and the different omics measurements were obtained from the same biological samples, which facilitates the integration and analysis of data using covariance-based methods. We validate our dataset by showing that ChIP-seq, RNA-seq and metabolomics signals recapitulate existing knowledge about the response of ribosomal genes and the contribution of trehalose metabolism to heat stress.</p>
Project description:To characterize the PTI response of tomato and the effect of the delivery of a subset of effectors, we performed an RNA-seq analysis of tomato Rio Grande prf3 leaves challenged with either the flgII-28 peptide or the following bacterial strains: Agrobacterium tumefaciens GV2260, Pseudomonas fluorescens 55, Pseudomonas putida KT2440, Pseudomonas syringae pv. tomato (Pst) DC3000, Pst DC3000 deltahrcQ-U deltafliC and Pst DC3000 deltaavrPto deltaavrPtoB. NOTE: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
Project description:Pathogen invasion in plants is associated with transcriptional reprogramming. Enigmatically, plants induce similar transcriptome responses upon infection by virulent or avirulent pathogens. This renders the importance of transcriptional reprogramming for immunity obscure. Here, using RNA-seq, we generate time-series transcriptome data coupled with genetic perturbations to reveal temporal dynamics upon infection by virulent or avirulent strains of a bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana. Fast and sustained transcriptional reprogramming occurs upon infection with avirulent strains while virulent strain infection leads to a slower response with comparable gene expression patterns and magnitudes. Importantly, transcriptome analysis of resistant and susceptible mutants responding to avirulent strains links delayed transcriptional reprogramming to compromised immunity. Taken together, our results pinpoint the early critical time window of transcriptional reprogramming for establishing effective immunity against the bacterial pathogen. Overall design: Leaves of Col-0 and all the single, double, triple and quadruple mutants of dde2-2, ein2-1, pad4-1, sid2-2 were syringe-infiltrated with mock (water) or suspensions of Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) carrying an empty vector (pLAFR), Pto DC3000 carrying AvrRpt2, or Pto DC3000 carrying AvrRpm1 at the OD600 of 0.001. Similarly, leaves of the rpm1-3 rps2-101C mutant plants were inoculated with mock, Pto DC3000 carrying AvrRpt2 or Pto DC3000 carrying AvrRpm1. Three fully-expanded leaves (leaves 7-9) from three different plants were harvested as a single biological replicate at 1, 2, 3, 4, 6, 9, 12, 16, 20, 24, 36, 48 hours post inoculation (hpi). To generate three biological replicates, three independent experimental trials were carried out, in which plant positions within pots and growth chambers were randomized in order to avoid undesirable systematic effects. For the statistcal analysis, 348 samples (M001-M348) were used.
Project description:To gain an insight into molecular mechanisms underlying plant-microbe interactions gene expression changes in rice plants in response to a plant growth promoting rhizobacteria such as the Pseudomonas putida, root transcriptome analysis through microarray technology was performed from rice roots in response to P. putida RF3. Species of Pseudomonas are well known as biocontrol agents hence defense response and genes related to root exudation of phytochemicals were analysed in detail. For treatment of rice plants with P. putida, aseptically germinated rice seedlings from half strength MS medium were transferred to flasks containing Hoaglands’ nutrient solution, treated with P. putida and incubated for 48 hours in growth chamber in an orbital shaker. Gene expression changes in rice roots were then analyzed by microarray experiment. Untreated roots served as control. Data analysis revealed defense responsive genes to be upregulated with greater fold changes. In addition to defense response genes, few genes involved in secondary metabolism were also upregulated significantly. Validation of microarray data was performed using real time PCR for defense responsive genes (OsPBZ, OsPR101a, OsCHIA, etc). Detailed analysis of the differentially expressed genes reveal the role of P. putida RF3 in inducing systemic resistance in plants thereby immunizing the rice plants against future attacks by pests/pathogens. Our study enhances the current understanding on gene expression changes occurring during plant-microbe associations and thus demonstrates the potential of P. putida RF3 as a biocontrol agent. Overall design: control root vs root tissue treated with PGPR