Hr-Transcriptomic analysis of the localized acquired resistance (LAR) phenomenon in Arabidopsis thaliana
ABSTRACT: tri38-lar - hr - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Here, we want to analyse the transcriptome of Arabidopsis thaliana developing HR. To achieve this, we used Col0 leaf tissues developing an HR reaction after inoculation of the avirulent strain of PstDC3000 carrying the gene avrRpm1. Keywords: normal vs disease comparison Overall design: 1 dye-swap - CATMA arrays
Project description:tri38-lar - hr - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Here, we want to analyse the transcriptome of Arabidopsis thaliana developing HR. To achieve this, we used Col0 leaf tissues developing an HR reaction after inoculation of the avirulent strain of PstDC3000 carrying the gene avrRpm1. Keywords: normal vs disease comparison 1 dye-swap - CATMA arrays
Project description:tri38-lar - lar - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Plants were treated either with PstDC3000 (avrRpm1)or MgCl2 (control plants). The samples were studied at 3 points of the infection kinetics of the LAR phenomenon: 6h, 24h and 48h. Keywords: normal vs disease comparison 3 dye-swaps - CATMA arrays 12 biological repetitions were pooled for this experiment.
Project description:tri38-lar - lar - Analyse the transcriptome of Arabidopsis thaliana plants developing localized acquired resistance (LAR) and a hypersensitive response (HR). The goal is to identify genes inducing LAR and/or HR. Plants were treated either with PstDC3000 (avrRpm1)or MgCl2 (control plants). The samples were studied at 3 points of the infection kinetics of the LAR phenomenon: 6h, 24h and 48h. Keywords: normal vs disease comparison Overall design: 3 dye-swaps - CATMA arrays 12 biological repetitions were pooled for this experiment.
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:Innate immune responses of plant cells confer the first line of defence against pathogens. Signals generated by activated receptors are integrated inside the cell and converge on transcriptional programmes in the nucleus. In Arabidopsis, the CAMTA family of transcription factors plays a pivotal function in immunity. CAMTA binding motifs are highly enriched in the genes quickly induced during ETI and PTI. Using RNA-seq, we investigated the role of CAMTA TFs during the early ETI and PTI transcriptional responses. Overall design: We compared the expression changes between an Arabidopsis mutant line carrying the camta3-D (sr1-4d) dominant negative mutation and Col-0 wild-type plants following treatment with the PAMP flg22 (100 nM), and the avirulent bacterial strains Pst DC3000 AvrRpm1 (OD600=0.001) and Pst DC3000 AvrRps4 (OD600=0.001). The expression changes were analysed at one time point after each treatment (1 hour for flg22 and 4 hours for Pst DC3000 AvrRpm1 and Pst DC3000 AvrRps4 treatments).
Project description:Compare gene expression in the resting leaves of Arabidopsis thaliana WT with the mutants fou2 and tpc1-2. To analyse the contribution of the fou2 and tpc1-2 mutations in Arabidopsis thaliana to gene expression, transcript levels in the resting leaves of Arabidopsis were measured using 4 weeks-old plants grown in control conditions (long day).
Project description:With frequent fluctuations in global climate, plants often experience co-occurring dry-wet cycles and pathogen infection and this combination adversely affects plant survival. In the past, some studies indicated that morpho-physiological responses of plants to the combined stress are different from the individual stressed plants. However, interaction of drought stressed or drought recovered plants with pathogen has not been widely studied at molecular level. Such studies are important to understand the defense pathways that operate as part of combined stress tolerance mechanism. In this study, Arabidopsis plants were exposed to individual drought stress (soil drying at 40% FC, D), Pseudomonas syringae pv tomato DC3000 (PStDC3000), infection and their combination. Plants recovered from drought stress were also exposed to PStDC3000. Beside we have also infiltrated P. syringae pv tabaci (PSta, non-host pathogen) individually or in combination with drought stress. Using Affymetrix WT gene 1.0 ST array, global transcriptome profiling of plants leaves under individual drought stress and pathogen infection was compared with their combination. Results implicate that plants exposed to combined drought and pathogen stress experience a new state of stress where each combination of stressor and their timing defines the plant responses and thus should be studied explicitly. Global transcriptional analysis in Arabidopsis leaves exposed to individual and combined drought and pathogen stress. Overall design: Microarray based global gene expression analysis was carried out in Arabidopsis leaves after exposure to individual and combined stress treatments. Arabidopsis plants were exposed to drought stress (D), PStDC3000 infection (P, 1d and 6d), PSta infection (NH, 1d). For treatments involving combined stress, PStDC3000 was infiltrated on drought stressed plants (DP, 1d), plants were exposed to drought stress upon PStDC3000 infiltration (PD, 1d), PSta was infiltrated on drought stressed plants (DNH, 1d), and PStDC3000 was infiltrated on drought recovered plants (DRP). Six plants per treatment were used such that leaf tissue from three plants made one biological replicate. Two biological replicates were hybridized for each treatment.
Project description:Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. The presented model is a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. The Petri net formalism was used to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs were applied. Based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism, the core metabolism of Arabidopsis thaliana was formulated. Each reaction (transition) is experimentally proven. The complete Petri net model consists of 134 metabolites, represented by places, and 243 reactions, represented by transitions. Places and transitions are connected via 572 edges.
Project description:The present work is directed at studying changes at the proteome level in Arabidopsis thaliana leaves in response to Pseudomonas syringae virulent (Pst) and avirulent (Pst avrRpt2) strains. Arabidopsis leaves were sampled from challenged plants at 4, 8 and 24 hours post inoculation. Proteins were TCA-acetone-phenol extracted and subjected to 2-DE (5-8 pH range) and MS/MS (MALDI-TOF-TOF) analysis. Out of 800 matched spots on each of the 36 gels analysed, 147 spots were either absent in at least one of the conditions studied (time or treatments; qualitative variable spots) or differentially accumulated between time and treatments (quantitative variable spots). Out of the 24 proteins successfully identified over TAIR10 database, 23 have not been reported previously in similar proteomics studies of the Arabidopsis thaliana-Pseudomonas syringae interaction. The exhaustive statistical analysis performed, including principal component and heat map, showed that 24 hours post inoculation can clearly discriminate the challenged plants from the control. The protein change occurred early (4 hours post inoculation) following the virulent pathogen infection, whereas the change occurred later (24 hours post inoculation) following the avirulent pathogen inoculation. Concerning the variable proteins, three behavioural groups can be observed: group 1 (common protein changes in response to virulent and avirulent pathogen infection), group 2 (protein changes in response to virulent pathogen infection) and group 3 (protein changes in response to avirulent pathogen infection). Differential identified proteins following the pathogen infection belonged to different groups including those of oxidative stress defence, enzymes of metabolic pathways and molecular chaperones.
Project description:This model is from the article:
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M.
J Theor Biol.2011 Aug 21;283(1):152-67.
Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.