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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomes and differential gene expression analysis of the Arabidopsis cells that received type-III effectors delivered by Xanthomonas campestris pv. Campestris (Xcc) bacterial mutants

ABSTRACT: Due to low numbers and poor accessibility of host cells that are targeted for effector delivery, the actual biological functions of most effectors remain elusive. Here, we developed a novel Isolation Nuclei TArgeted by Bacterial Effectors (INTABE) system, which facilitates selectively recovering nuclei of the cells in Arabidopsis thaliana plants that have received type-III effectors of pathogenic Xanthomonas bacteria. Using these nuclei as studying materials, we analysed changes in host gene expression and their correlation with changes in DNA methylation induced by Xanthomonas effector Outer Protein D (XopD).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Yuan You

PROVIDER: E-MTAB-10280 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The eINTACT system dissects bacterial exploitation of plant osmosignalling to enhance virulence.

You Yuan Y Koczyk Grzegorz G Nuc Maria M Morbitzer Robert R Holmes Danalyn R DR von Roepenack-Lahaye Edda E Hou Shiji S Giudicatti Axel A Gris Carine C Manavella Pablo A PA Noël Laurent D LD Krajewski Paweł P Lahaye Thomas T

Nature plants 20221222 1

Bacteria inject effector proteins into host cells to manipulate cellular processes that promote disease. Since bacteria deliver minuscule amounts of effectors only into targeted host cells, it is technically challenging to capture effector-dependent cellular changes from bulk-infected host tissues. Here, we report a new technique called effector-inducible isolation of nuclei tagged in specific cell types (eINTACT), which facilitates affinity-based purification of nuclei from Arabidopsis plant ce ...[more]

PMID: 36550363

Similar Datasets

DNA methylation profiling and analysis of differentially methylated regions (DMRs) of the Arabidopsis cells that received type-III effectors delivered by Xanthomonas campestris pv. Campestris (Xcc) bacterial mutants

Project description:Due to low numbers and poor accessibility of host cells that are targeted for effector delivery, the actual biological functions of most effectors remain elusive. Here, we developed a novel Isolation Nuclei TArgeted by Bacterial Effectors (INTABE) system, which facilitates selectively recovering nuclei of the cells in Arabidopsis thaliana plants that have received type-III effectors of pathogenic Xanthomonas bacteria. Using these nuclei as studying materials, we analysed changes in host gene expression and their correlation with changes in DNA methylation induced by Xanthomonas effector Outer Protein D (XopD).

2022-10-22 | E-MTAB-10281 | biostudies-arrayexpress

Transcriptomics of Xanthomonas campestris pv campestris in cabbage xylem sap

Project description:Xylem sap of young cabbage plantlets was recovered from root pressure exudation and used as a growth medium for the vascular pathogen Xanthomonas campestris pv campestris, the causative agent of the black rot of Brassicaceae.

2014-01-04 | E-MTAB-2290 | biostudies-arrayexpress

Early transcriptional response to phytopathogen Xanthomonas campestris pv. campestris by susceptible cabbage host

Project description:Black rot, caused by Xanthomonas campestris pv. campestris (Xcc) is one of the most devastating diseases of cruciferous crops worldwide. The pathogen infects and multiplies in plant vascular tissues and, as the disease progresses, the veins of infected tissues turn black and characteristic V-shaped lesions appear along the margins of leaves.The aim of this work is to identify differentially expressed genes from Brassica oleracea during early infection by Xcc, in an attempt to identify proteins related to resistance. Cabbge seedlings were inoculated with Xanthomonas campestris pv campestris (Xcc) suspension and cabbage gene expression at 6h., 24h. And 48h. After inoculation was assessed with help of Brassica 95k EST microarray chip.

2015-05-09 | E-GEOD-68670 | biostudies-arrayexpress

Xanthomonas campestris pv. campestris 8004: wild type vs. ravA (or ravS or ravR) mutant

Project description:Transcriptional profiling of Xanthomonas campestris pv. campestris 8004 comparing control wild type strain with ravA (or ravS or ravR) mutant The effects of mutating ravS, ravR and ravA on EPS synthesis, biofilm production and motility were very different , the factors responsible for these differences are not clear. With comparative analysis of the regualtion pathways by RavS, RavR and RavA, we can indentify different genes regulated by these three genes and maybe explain the different phenotypes caused by these genes mutations. Comparative analysis of the regualtion pathways by RavS, RavR and RavA Two-condition experiment, wild type vs. mutants. Biological replicates were independently grown and harvested. One replicate per array

2012-10-10 | E-GEOD-32908 | biostudies-arrayexpress

Comparative microarrays of Xanthomonas campestris pv. camp. B100 Δcrt1 with the Xanthomonas camp. pv camp B100

Project description:To investigate the effect of the transcriptional regulator Crt1 on the transcirptome of Xanthomonas campestris pv. camp (Xcc), comparative genome-wide transcriptome analysis was conducted. For this purpose, the wild-type strain Xcc B100 and the mutant strain Xcc Δcrt1 were each cultivated in triplicates in minimal medium supplemented with glucose as sole carbon source. RNA samples from the biological replicates were obtained at an early stationary growth stage. RNA was isolated and the three replicates were combined for each strain. Furthermore, the data from two arrays (dye swap) were combined to provide statistically reliable conclusions.

2022-10-25 | E-MTAB-12383 | biostudies-arrayexpress

A proteomic approach to study Brassica oleracea responses to black rot (Xanthomonas campestris pv. campestris), part 1

Project description:Understanding plant’s response mechanisms against pathogenesis is fundamental for the development of resistant crop varieties and more productive agriculture. In this regard, ‘omic’ approaches are heralded as valuable technologies. In this work, combining iTRAQ technology with mass spectrometry, the proteomes from leaves of Brassica oleracea plants infected with Xanthomonas campestris pv. campestris (Xcc) and control plants at two different post-infection times were compared.

2022-02-23 | PXD009097 | Pride

A proteomic approach to study Brassica oleracea responses to black rot (Xanthomonas campestris pv. campestris), part 2

2022-02-23 | PXD009098 | Pride

Xanthomonas campestris pv. campestris str. 8004 (Xcc 8004; Indian Isolate): Wild type vs xibR mutant, under the both iron-replete and iron-deplete conditions.

Project description:Transcriptional profiling of low-iron stimulon and XibR influenced regulon using wild-type Xcc 8004 and xibR mutant grown under iron-replete and iron-deplete conditions. Trancriptional analysis under iron-deplete condition, mimicking in planta environment, provides greater insights into expression pattern of several virulence-associated functions under low-iron. A genetic screen sggested the involvement of XibR (Xanthomonas iron binding regulator) in iron-uptake and metabolism. Present transcriptional analysis suggested the co-regulation of virulence associated functions including siderophore biosynthesis, motility, chemotaxis and typeIII effectors by a novel transcriptional regulator of NtrC family protein XibR and iron avability.

2016-11-02 | GSE89267 | GEO

Transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering

Project description:We investigated the transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering using INTACT reporter lines. Samples were collected in four biological replications.

2017-05-21 | E-MTAB-5130 | biostudies-arrayexpress

Host transcriptional reprogramming in response to the rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae strain BLS354

Project description:We performed RNA-Seq of leaves of Oryza sativa L. ssp. japonica cv. Nipponbare 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354, the causal agent of bacterial leaf streak. Results provide insight into the molecular basis of bacterial leaf streak, particularly the role of transcription activator-like effectors in the disease. Examination of mRNA levels in Oryza sativa L. ssp. japonica cv. Nipponbare leaves at 48 hours after inoculation with Xanthomonas oryzae pv. oryzicola strain BLS354 with three biological replicates compared to three replicates of mock inoculated O. sativa as the control.

2016-07-07 | E-GEOD-75131 | biostudies-arrayexpress

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