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Biological function of Pip3

ABSTRACT: Ralstonia solanacearum is the causal agent of bacterial wilt. Arabidopsis thaliana monogenic resistance to the strain GMI1000 is conferred by the RRS1-R gene, present in the resistant ecotype ND-1 and absent in the susceptible ecotype Col-0. The corresponding protein is recognized by the avirulence protein PopP2 of R. solanacearum. In order to identify the plant proteins involved in the PopP2/RRS1-R perception complex, the screening of a root cDNA library in yeast was performed using PopP2 as bait. One interactor found was called Pip3, and we would like to better understand its biological function. Thereby we choose to compare two RNAi lines with their wild type Nd-1 background, and one KO line with its wild type Col-0 background. Also, two overexpressor lines will be compared with their wilt type Nd-1 background and two with their Col-0 background.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE19273 | GEO | 2009/12/10

SECONDARY ACCESSION(S): PRJNA120951

REPOSITORIES: GEO

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Biological function of Pip3

Project description:Ralstonia solanacearum is the causal agent of bacterial wilt. Arabidopsis thaliana monogenic resistance to the strain GMI1000 is conferred by the RRS1-R gene, present in the resistant ecotype ND-1 and absent in the susceptible ecotype Col-0. The corresponding protein is recognized by the avirulence protein PopP2 of R. solanacearum. In order to identify the plant proteins involved in the PopP2/RRS1-R perception complex, the screening of a root cDNA library in yeast was performed using PopP2 as bait. One interactor found was called Pip3, and we would like to better understand its biological function. Thereby we choose to compare two RNAi lines with their wild type Nd-1 background, and one KO line with its wild type Col-0 background. Also, two overexpressor lines will be compared with their wilt type Nd-1 background and two with their Col-0 background. 27 samples were used in this experiment.

2009-12-09 | E-GEOD-19273 | biostudies-arrayexpress

Expression analysis of Ralstonia solanacearum strain GMI1000 at 20°C and 28°C in rich medium (CPG) and in planta

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Expression analysis of Ralstonia solanacearum strain GMI1000 at 20°C and 28°C in rich medium (CPG) and in planta

Project description:Investigation of whole genome gene expression level changes in the bacterial wilt pathogen Ralstonia solanacearum, strain GMI1000 at 20°C and 28°C in culture and in planta. The tropical strain GMI1000 cannot wilt tomato plants at 20°C although it can cause full-blown disease at 28°C. A 16 array study using total RNA recovered from the following: 8 separate cultures of Ralstonia solanacearum strain GMI1000 grown in rich medium-CPG (4 grown at 20°C and 4 grown at 28°C) 8 separate in planta samples of Ralstonia solanacearum strain GMI1000 harvested from diseased tomato plants cv. BonnyBest (4 recovered from plants grown at 20°C and 4 from plants grown at 28°C) Each array (4-plex format) measures the expression level of 5061 genes from Ralstonia solanacearum strain GMI1000 with 2 to 6, 40-70 mer probes per gene, with two-fold technical redundancy. The arrays also contain probes for intergenic regions with no technical replicates.

2012-01-15 | E-GEOD-33657 | biostudies-arrayexpress

Transcriptom analysis of the interaction Medicago truncatula – Ralstonia solanacearum

Project description:affy_ralstonia_medicago - Ralstonia solanacearum is the causal agent of the devastating bacterial wilt disease. Its infection process was studied with an in vitro inoculation procedure on intact roots of Medicago truncatula. The pathosystem involved susceptible A17 and resistant F83005.5 M truncatula lines infected with the pathogenic strain GMI1000. The mutant A17 line, Sickle, which showed a resistant phenotype was also part of the experiment. To identify host signaling pathway triggered by R. solanacearum infection with a focus on the involvment of ethylene, we used the Medicago Affymetrix array to monitore the expression profiles and the molecular process associated with initial symptoms development (12hpi) and colonization (72hpi). In order to maximize chances to observe differential gene expression, RNA samples were extracted from the root infection zone (root tips) -Three Medicago truncatula lines, A17, F83005.5 and sickle were inoculated with GMI1000 Ralstonai solanacearum strain (107 cfu/ml). RNA were extracted from root extremities (1 cm above the root tip) at time 0, 12h and 72h post inoculation. Three biological repeats were conducted

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Transcript data affected by natural variation or PME17 mutation in Arabidopsis thaliana, infested or not with the aphid Myzus persicae

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Transgenic Arabidopsis expressing AtMYB23SRDX

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Expression data from Arabidopsis thaliana Col-0 challenged with Ralstonia solanacearum race 4 (roots)

Project description:Bacterial wilt caused by Ralstonia solanacearum is a serious seed/soil borne disease that causes severe yield and quality losses in many plants. In order to understand the change in genome expression of inculated plants, microarray analysis were performed. Twenty one days old roots of Arabidopsis Col-0 were inoculated with Ralstonia solanacearum race 4 @ 10^9 & 10^8 cfu/ml in different plants, distil water were mock inoculated, after five days plants were taken for RNA extraction and hybridization on Affymetrix microarrays. Plants were incubated in growth chamber for disease development, temperature and humidity were maintained as per plant requirement for both treated and control plants.

2016-12-21 | GSE92631 | GEO

Effect of nitrogen compounds on imbibed mutant seeds impaired in glucosinolate biosynthesis

Project description:These RNAseq data are from germinating cyp79B2, cyp79B3, myb28, myb29 (qko), cyp79B2, cyp79B3 (cyp) and myb28 myb29 (myb) mutant seeds. Col-0 genotype was used as the Arabidopsis' WT reference ecotype and all mutant seeds are from the Col-0 genetic background. Samples were sown on agarose 0,8%, supplemented or not by nitrate KNO3 10Mm or potassium thiocyanate KSCN 8µM. RNA isolation was performed using NucleoSpin® RNA Plant and Fungi kit. RNA quantification was obtained with a NanoDrop ND-100 (NanoDrop Technologies, DE, USA) and the RNA Integrity was measured with a 4100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). cDNA library construction and sequencing were performed with DNBseq™ technology at Beijing Genomics Institute BGI. FastQC was used to check read quality, mapping analysis and transcript quantiifcation were performed using a quasi-mapping alignment from Salmon.

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Response of clavata 2-7 mutant to Ralstonia solanacearum.

Project description:In this experiment, we compared transcriptome of one knock out mutants in the CLV2 gene (clv2-7) to his wild type Col-0 when challenged with the virulent GMI1000 strain of Ralstonia solanacearum. This mutant shows a significant delay of symptom appearance. The experiment was conducted on roots and leaves of 4 week old plants harvested at the time of inoculation and when the first symptoms appeared on the susceptible wild type (4 days after inoculation - 25% of wilted leaves: disease index 1, D1).

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