Transcription profiling of Nicotinan benthamiana in response to Pectobacterium carotovorum WPP14 and Pseudomonas syringae pv. tomato DC3000
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ABSTRACT:
ORGANISM(S): Nicotiana benthamiana
SUBMITTER: Amy Charkowski
PROVIDER: E-TABM-752 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Plant defenses against pathogens and insects are regulated differentially by cross-communicating signaling pathways in which salicylic acid (SA), jasmonic acid (JA) and ethylene (ET) play key roles. To understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of SA, JA, and ET signaling in Arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack. Arabidopsis plants were exposed to a pathogenic leaf bacterium (Pseudomonas syringae pv. tomato), a pathogenic leaf fungus (Alternaria brassicicola), tissue-chewing caterpillars (Pieris rapae), cell-content-feeding thrips (Frankliniella occidentalis), or phloem-feeding aphids (Myzus persicae). Monitoring the signal signature in each plant-attacker combination showed that the kinetics of SA, JA, and ET production varies greatly in both quantity and timing. Analysis of global gene expression profiles demonstrated that the signal signature characteristic of each Arabidopsis-attacker combination is orchestrated into a surprisingly complex set of transcriptional alterations in which, in all cases, stress-related genes are overrepresented. Comparison of the transcript profiles revealed that consistent changes induced by pathogens and insects with very different modes of attack can show considerable overlap. Of all consistent changes induced by A. brassicicola, P. rapae, and F. occidentalis, more than 50% were also induced consistently by P. syringae. Notably, although these four attackers all stimulated JA biosynthesis, the majority of the changes in JA-responsive gene expression were attacker-specific. All together our study shows that SA, JA, and ET play a primary role in the orchestration of the plant's defense response, but other regulatory mechanisms, such as pathway cross-talk or additional attacker-induced signals, eventually shape the highly complex attacker-specific defense response. In the experimental set up we intended to select for genes that showed a more than 2-fold change in the same direction(up or down)at two time points after pathogen or insect attack. The results are described in the following paper:; De Vos, M., Van Oosten, V.R., Van Poecke, R.M.P., Van Pelt, J.A., Pozo, M.J., Mueller, M.J., Buchala, A.J., Metraux, J.-P., Van Loon, L.C., Dicke, M. and Pieterse, C.M.J. (2005). Signal signature and transcriptome changes in Arabidopsis upon pathogen and insect attack. Molecular Plant-Microbe Interactions. Experimenter name = Corne Pieterse; Experimenter phone = +31 30 253 3013; Experimenter fax = +31 30 251 8366; Experimenter department = Section Phytopathology; Experimenter institute = Utrecht University; Experimenter address = Department of Biology; Experimenter address = Utrecht University; Experimenter address = Sorbonnelaan 16; Experimenter address = Utrecht; Experimenter zip/postal_code = 3584CA; Experimenter country = The Netherlands Experiment Overall Design: 14 samples were used in this experiment
2008-06-13 | E-GEOD-5525 | biostudies-arrayexpress
Project description:Genome-wide in planta determination of the quorum sensing regulon in Pectobacterium atrosepticum, through gene expression analysis of ExpI mutants using Agilent custom microarrays.
2008-07-01 | E-TABM-384 | biostudies-arrayexpress
Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Pectobacterium upon treatment of polyphenol compound.
2022-10-05 | GSE196675 | GEO
Project description:RNA-seq of Arabidopsis thaliana spermine synthase (spms) mutant and wild-type (Col-0) inoculated with Pseudomonas syringae pv. tomato DC3000 or mock (MgCl2)
2023-08-31 | E-MTAB-13086 | biostudies-arrayexpress
Project description:Pectobacterium are Gram-negative rods of the family Pectobacteriaceae. They are the causative agent of soft rot diseases of crops and ornamental plants. However, their virulence mechanisms are not yet fully elucidated. Membrane vesicles (MVs) are universally released by bacteria and are be-lieved to play an important role in pathogenicity, and survival of bacteria in the environment. Our study investigates the role of MVs in the virulence of Pectobacterium. The results indicate that the morphology and yields of MVs depend on medium composition. In polygalacturonic acid (PGA) supplemented media, Pectobacterium produce MVs of a larger size (100-300 nm) apart of vesicles below 100 nm. Proteomic analyses revealed the presence of pectate degrading enzymes in MVs. The pectate plate test and enzymatic assay proved that those enzymes are active and able to de-grade pectates. What is more, pathogenicity test indicated that MVs derived from Pectobacterium were able to induce maceration of Zantedeschia sp. leaves. We also show that MVs of β-lactamase producing strains were able to suppress ampicillin activity and permit the growth of susceptible bacteria. Those findings indicate that MVs of Pectobacterium play an important role in host-pathogen interactions and niche competition with other bacteria. Our research also sheds some light on the mechanism of MVs production. We demonstrate that Pectobacterium strains, which overexpress the green fluorescence protein (GFP), produce more MVs than wild type strains. Moreover, proteomic analysis revealed that GFP was present in MVs. Therefore, we demonstrate that protein sequestration into MVs is not limited strictly to periplasmic proteins and is a common occurrence. Our research highlights the importance of MVs production as a mechanism of cargo delivery in Pectobacterium and an alternative secretion system.
2022-02-15 | PXD029090 | Pride
Project description:This proposal is aimed at providing transcriptome data to underpin a long-term joint research programme of Steve Smith and Alison Smith. We are jointly studying starch synthesis and breakdown in Arabidopsis leaves, and individually studying other enzymes of carbohydrate metabolism (eg. sucrose synthases, invertases, sugar transporters). Collectively these enzymes are encoded by up to 100 known genes, but there are many others of relevance to our studies. For several years we have employed a defined set of growth conditions for this work (resulting in numerous publications). We have extensive data for changes in the amounts of starch, malto-oligosaccharides and sugars throughout the diurnal cycle in these plants, and we intend to quantitate numerous key enzymes. We now wish to profile changes in transcripts in these plants, so that this information can be correlated with changes in the amounts of key enzymes and metabolites. Analysis of the data sets will help us to relate the synthesis of certain enzymes to particular metabolic functions, and also to help identify genes encoding novel proteins involved in carbohydrate metabolism. Current research is aimed at discovering such novel proteins using proteomics approaches (BBSRC Grant: _Discovery and Functional Analysis of the Starch Proteome_). While the growth conditions (12h photoperiod, 150 umol/m2/s, 20C) and ecotype (Col-0) are specifically tailored to our experiments, they will be of value to the wider community, and could form the basis for collaborative studies with other groups. The experiment has involved sampling leaves at eleven different time points as follows: 0, 1, 2, 4, 8, 12, 13, 14, 16, 20, and 24 h (where time 0 is the onset of dark and 12 h is the onset of light). The 24 h time point is a repeat of 0 h. This sequence provides relatively more samples immediately after the light-dark transitions, when changes in metabolism are most pronounced. Plants were grown in a controlled environment chamber under defined conditions, and selected for harvest according to a random number generator. Three fully expanded leaves were harvested from each of 20 plants for each sample. Leaves were frozen at -80 C and a portion saved for metabolite and enzyme assays while RNA was isolated from the remainder. <br> This experiment was reloaded in February 2011, replacing the existing raw data files which had identifier problems with the original CEL files from ftp://arabidopsis.info/pub/NASCArrays/Data/By_Experiment_ID/Exp60/ and adding experimental factors.
2005-02-16 | E-NASC-49 | biostudies-arrayexpress
Project description:To investigate the mechanism under the cross protection between HLSV and TMV, microarray analysis was conducted to examine the transcriptional levels of global host genes during cross protection, using Tobacco Gene Expression Microarray, 4x44k slides. The transcriptional level of some host genes corresponded to accumulation level of TMV. Some host genes were up-regulated only by HLSV. The gene expression in Nicotiana benthamiana during cross protection was measured at 12 days post HLSV or mock buffer inoculated as well as TMV infected N. benthamiana which pre-inoculated HLSV or mock bufer at 3 dpi (which is equal to 15 dpi by HLSV).
2014-05-12 | E-GEOD-47180 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-01-10 | E-GEOD-51379 | biostudies-arrayexpress
Project description:Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media. The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369
2013-08-30 | GSE50468 | GEO
Project description:Whole genome analysis of gene expression by Pectobacterium atrosepticum strain SCRI1043 wildtype and its relA, expI and rpoS deletion mutants when grown to exponential and stationary phase in PMB media. The data is further described in Bowden et al (2013) Virulence in Pectobacterium atrosepticum is regulated by a coincidence circuit involving quorum sensing and the stress alarmone, (p)ppGpp. Molecular Microbiology. DOI: 10.1111/mmi.12369 A 24 chip study using total RNA recovered from three separate wild-type cultures of Pectobacterium atrosepticum SCRI1043 and three separate cultures from three single mutant strains of SCRI1043 possessing deletions within relA (ECA3569), expI (ECA0105) or rpoS (ECA3530) when grown in Pel Minimal Broth (PMB) media to log-phase (6h) or early stationary phase (14h) growth. Each chip measures the expression level of 4,472 genes from Pectobacterium atrosepticum SCRI1043 with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
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