Expression profiling of uninfected and Golovinomyces orontii infected Arabidopsis thaliana wild type Col-0 and del1-1 mutant
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Mary Wildermuth
PROVIDER: E-GEOD-40973 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Salicylic acid (SA) is a critical molecule mediating plant innate immunity with an important role limiting the growth and reproduction of the virulent powdery mildew (PM) Golovinomyces orontii on Arabidopsis thaliana. To investigate this later phase of the PM interaction, and the role played by SA, we performed replicated global expression profiling for wild type and SA biosynthetic mutant ics1 Arabidopsis from 0 to 7 days post infection. We found that ICS1-impacted genes comprise 3.8% of profiled genes with known molecular markers of Arabidopsis defense ranked very highly by the multivariate empirical Bayes statistic (T2 statistic ((Tai and Speed, 2006)). Functional analyses of T2-selected genes identified statistically significant PM-impacted processes including photosynthesis, cell wall modification, and alkaloid metabolism that are ICS1-independent. ICS1-impacted processes include redox, vacuolar transport/secretion, and signaling. Our data also supports a role for ICS1 (SA) in iron and calcium homeostasis and identifies components of SA crosstalk with other phytohormones. Through our analysis, 39 novel PMâimpacted transcriptional regulators were identified. Insertion mutants in one of these regulators, PUX2, results in significantly reduced reproduction of the powdery mildew in a cell death independent manner. Though little is known about PUX2, PUX1 acts as a negative regulator of Arabidopsis CDC48 (Rancour et al., 2004; Park et al., 2007), an essential AAA-ATPase chaperone that mediates diverse cellular activities including homotypic fusion of ER and Golgi membranes, ER-associated protein degradation, cell cycle progression, and apoptosis. Future work will elucidate the functional role of the novel regulator PUX2 in PM resistance. Experiment Overall Design: Arabidopsis whole leaves were harvested at 6h, 1 day, 3 days, 5 days and 7 days after Golovinomyces orontii infection for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. Gene expression profiles were obtained for wild type Columbia-0 and enhanced disease susceptibility mutant eds16-1, a null isochorismate synthase 1 (At1g74710) mutant. In parallel, uninfected samples were collected at 0 hr and 7days from wild type and mutant plants. The experiment includes 4 biological replicates.
2009-02-21 | E-GEOD-13739 | biostudies-arrayexpress
Project description:Obligate biotrophs such as the virulent powdery mildew Golovinomyces orontii alter plant host cellular architecture, metabolism, and defense in order to acquire nutrients while suppressing cell death and senescence. G. orontii exclusively infects epidermal cells of Arabidopsis with clearly defined stages of infection. Host factors mediating the powdery mildew (PM) interaction are often expressed in the mesophyll cells underlying the infected epidermal cells. Therefore, in order to identify Arabidopsis processes and regulators mediating this PM interaction, we used UV laser microdissection to isolate cells at the PM infection site for global expression profiling. As part of this process, we optimized and/or developed novel tissue preparation, RNA extraction and amplification, and quality control protocols resulting in highly correlated biological replicate data. We focused on the growth and reproduction stage of the PM infection (5 days post infection) when the number of reproductive structures, conidiophores, can be quantified. Site-specific profiling increased our sensitivity dramatically, allowing us to identify specific processes, process components, and their putative regulators hidden in previous whole leaf global expression analyses. For example, the known cell cycle regulator MYB3R4 exhibits altered expression at the site of infection, as do a subset of cell-cycle-associated genes. Furthermore, null myb3r4 mutants exhibit enhanced resistance to PM with reduced conidiophores per colony, suggesting cell cycle control plays an important role in the PM interaction. Experiment Overall Design: Arabidopsis whole leaves from wild type Columbia-0 and enhanced disease susceptibility mutant eds16-1, a null isochorismate synthase 1 (At1g74710) mutant were harvested at 5 days after Golovinomyces orontii infection, microwave-fixed, paraffin-embedded and sectioned. Groups of epidermal and mesophyll cells (~20 cells/group) surrounding the G. orontii infected epidermal cell were cut using a Leica AS laser microdissection (LMD) system. In parallel, groups of epidermal and mesophyll cells were collected from uninfected leaves at 5 days from wild type Arabidopsis. LMD-isolated cells, whole leaf, whole leaf amplified and tissue scrape samples were used for RNA extraction and hybridization to Affymetrix Arabidopsis ATH1 microarrays. Gene expression profiles were obtained for wild type from all samples and for ics1 mutant from LMD infected samples. The experiment includes 2 biological replicates.
2009-12-14 | E-GEOD-15680 | biostudies-arrayexpress
Project description:0.5 mM SA plus 0.02% Silwet or 0.02% Silwet (control) was sprayed on leaves of 3.5 week old Arabidopsis plants. Samples were harvested at 0 (prior to treatment) , 3, 6, 12, and 24 hours post treatment. A subset of these samples were processed. Arabidopsis plants grown in parallel under standardized conditions were treated with SA + Silwet or Silwet alone (control). Only mature leaves of the same developmental age were harvested using leaves from 2-4 plants, totalling ~0.2 grams per sample. Plants were not resampled. In our hands, experimental replicates are highly reproducible. This was an exploratory experiment to look for candidate genes impacted by exogenous SA treatment. We were only able to process a subset of samples and chose to process key time points, sacrificing replicates at each time point.
2011-11-03 | E-GEOD-33402 | biostudies-arrayexpress
Project description:Neonicotinoid insecticides control crop pests based on their action as agonists at the insect nicotinic acetylcholine receptor which accepts chloropyridinyl- and chlorothiazolyl- analogs almost equally well. In some cases, these compounds have also been reported to enhance plant vigor and (a)biotic stress tolerance, independent of their insecticidal function. However, this mode of action has not been specifically defined. Using Arabidopsis thaliana, we show that the neonicotinoid compounds, imidacloprid (IMI) and clothianidin (CLO), via their 6-chloropyridinyl-3-carboxylic acid and 2-chlorothiazolyl-5-carboxylic acid metabolites, respectively, induce salicylic acid (SA) – associated plant responses. SA is a phytohormone best known for its role in plant defense against pathogens and as an inducer of systemic acquired resistance; however, it can also modulate abiotic stress responses. These neonicotinoids effect a similar global transcriptional response to that of SA including genes involved in (a)biotic stress response. Furthermore, similar to SA, IMI and CLO induce systemic acquired resistance resulting in reduced growth of a powdery mildew pathogen. The action of CLO induces the endogenous synthesis of SA via the SA biosynthetic enzyme ICS1, with ICS1 required for CLO-induced accumulation of SA, expression of the SA marker PR1, and fully enhanced resistance to powdery mildew. In contrast, the action of IMI does not induce endogenous synthesis of SA. Instead, IMI is further bioactivated to 6-chloro-2-hydroxypyridinyl-3-carboxylic acid, which is shown here to be a potent inducer of PR1 and inhibitor of SA-sensitive enzymes. Thus, via different mechanisms, these chloropyridinyl- and chlorothiazolyl- neonicotinoids induce SA responses associated with enhanced stress tolerance. response to neonicotinoid insecticides
2010-09-13 | E-GEOD-20188 | biostudies-arrayexpress
Project description:In plants, the activation of immunity is often inversely correlated with growth. Mechanisms that plant growth in the context of pathogen challenge and immunity are unclear. Investigating Arabidopsis infection with the powdery mildew fungus, we find that the Arabidopsis atypical E2F DEL1, a transcriptional repressor known to promote cell proliferation, represses accumulation of the hormone salicylic acid (SA), an established regulator of plant immunity. DEL1 deficient plants are more resistant to pathogens and slightly smaller than wild type. The resistance and size phenotypes of DEL1 deficient plants are due to the induction of SA and activation of immunity in the absence of pathogen challenge. Moreover, Enhanced Disease Susceptibility 5 (EDS5), a SA transporter required for elevated SA and immunity, is a direct repressed target of DEL1. Together, these findings indicate that DEL1 control of SA levels contributes to regulating the balance between growth and immunity in developing leaves.
2014-04-30 | GSE40973 | GEO
Project description:Phytohormones control many vital biological processes within plants, including growth and development, senescence, seed setting, fruit ripening and innate immunity. These biological processes are controlled by specific combinations of multiple phytohormones. The three main phytohormones involved in plant innate immunity are salicylic acid (SA), jasmonic acid (JA) and ethylene (ET). SA is produced in response to biotrophic and hemibiotrophic pathogens. Whereas, JA and ET are produced in response to necrotrophic pathogens. Pseudomonas aeruginosa is found ubiquitously within the environment, and has been shown to participate in both beneficial and pathogenic interactions with host plants depending on bacterial strain and environment. In this study, we found that Brassica napus (canola) seedlings infected with P. aeruginosa strain PA14 displayed symptoms of disease and had significant weight loss in both root and shoot. Our transcriptomic data revealed that many molecular processes involved in plant innate immunity were upregulated, whereas photosynthesis was downregulated.
2020-02-14 | E-MTAB-7864 | biostudies-arrayexpress
Project description:Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome. Three weeks old Arabidopsis (Col-0) plants were inoculated with either the avirulent isolate Emoy2 (incompatible interaction) or the virulent isolate Waco9 (compatible interaction) of Hpa, and infected plants were harvested at 1, 3 and 5 days post-inoculation (dpi) for total RNA extraction. mRNA profiles were generated by deep sequencing on Illumina GAIIx using EXPRSS tag-seq protocol. Each biological replicate set of samples were sequenced as one batch (biorep1, biorep2 and biorep3 in filenames) and each batch was sequenced in 4 individual Illumina flowcell lanes (lane1 to lane4 in filenames). Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. Emoy2 1, 3 and 5 dpi samples and Waco9 1 dpi samples were made two different codes (lib1 and lib2 in filenames) to generate higher depth of sequencing data. Each biological replicate set of samples were sequenced as one batch and each batch was sequenced in 4 individual Illumina flowcell lanes. Four sequecing lanes of each three biological repliates resulted in 12 sequencing libraries. 'The unassigned read_*' samples are for 'nobarcode_biorep[x]_lanne[x].fq' file containing sequences unassigned to any barcode from respective bioreplicate sequencing lanes.
2014-11-21 | E-GEOD-53641 | biostudies-arrayexpress
Project description:We report raw bulk RNA sequencing data of rice root sections from Meristem, Elongation and Maturation zones. For each section, we include 6 biological replicates. We also include the whole-root samples that include all developmental zones. The genes with enriched expression in certain developmental zones were used as developmental stage markers for our following single-cell RNA sequencing annotation.
2024-07-01 | E-MTAB-13889 | biostudies-arrayexpress
Project description:Pathogens target phytohormone signalling pathways to promote disease. Plants deploy salicylic acid (SA) mediated defences against biotrophs. Pathogens antagonise SA immunity by activating jasmonate signalling, e.g. Pseudomonas syringae pv. tomato DC3000 produces coronatine (COR), a jasmonate (JA) mimic. This study found unexpected dynamics between SA, JA and COR and co-operation between JAZ jasmonate repressor proteins during DC3000 infection. JA did not accumulate until late in the infection process and was higher in leaves challenged with coronatine deficient P. syringae or in the more resistant JA receptor mutant coi1. JAZ regulation was complex and coronatine alone was insufficient to sustainably induce JAZs. RNA was extracted from leaves of wild type Col-0 or the jaz5/10 mutant plants from leaves 6, 8, 12 or 16 hours after challenged with Pseudomonas syringae pv. tomato DC3000.
2015-08-28 | E-GEOD-72461 | biostudies-arrayexpress
Project description:Activation of plant immunity is associated with dramatic transcriptome reprogramming to prioritise immune responses over normal cellular functions. Changes in gene expression are coordinated by the immune hormone salicylic acid (SA). Here we investigated the involvement of the HECT-type ligase Ubiquitin Protein Ligase 3 (UPL3) in SA-induced transcriptional reprogramming. We show that UPL3 acts as an amplifier of SA-induced changes in gene expression. Four-week old Arabidopsis thaliana plants of wild-type Col-0 and mutant upl3-4 genotypes were germinated on soil in 100% relative humidity. After 12 days plants were transplanted to larger pots (six plants per pot) and grown for an additional 3 weeks before experimental treatment. Plants were continuously grown in an environmental chamber with 16/8 hour day/night light regime (120 mol m-2 s-1 light intensity), 21/18 degrees celcius day/night cycle and 65% relative humidity. Plants were then sprayed with water or 0.5 mM SA until all leaves were thoroughly covered with fine droplets. After 24 hours leaf tissue was harvested from 6 plants per treatment and pooled together into a single biological repeat. In total two or three independent biological repeats were collected. After harvesting leaf tissue was immediately frozen in liquid nitrogen until further analysis.
2018-11-09 | E-MTAB-7374 | biostudies-arrayexpress