Expression analysis of Arabidopsis thaliana Col-0 and parg1 with and without PARP inhibitor (3AB, 3MB), with and without MAMP (flg22, elf18)
ABSTRACT: Genome-wide gene expression analysis of the effects of PARP inhibitor (3AB) and, separately, a parg1 knockout, on early microbe-associate molecular pattern (MAMP)-induced gene expression in the plant basal defense response. Arabidopsis thaliana wild-type (Col-0), 3AB-treated and parg1-2 T-DNA knockout plants responding to the MAMP elicitors flg22 or elf18 were studied. The mutant and PARP inhibitors analyzed in this study are further described in Adams-Phillips, L.,C., Briggs, A.,G., Bent, A., F. 2010. Disruption of poly(ADP-ribosyl)ation mechanisms alters responses of Arabidopsis to biotic stress. Planty Physiol. 152(1):267-80 DOI: 10.1104/pp.109.148049. Overall design: A 27 chip study using total RNA recovered from three separate wild-type extracts of Arabidopsis Col-0 and three separate cultures of a parg1-2 knockout strain, in which a TDNA insertion has knocked out expression of At2g31870, treated for 1 hour with vehicle, flg22, elf28, 3AB, or 3MB. Each chip measures the expression level of 30,387 genes from Arabidopsis thaliana Col-0 with 6 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy and three-fold biological redundancy.
Pharmacological inhibition of poly(ADP-ribose) polymerase (PARP) or loss of Arabidopsis thaliana PARG1 (poly(ADP-ribose) glycohydrolase) disrupt a subset of plant defenses. In the present study we examined the impact of altered poly(ADP-ribosyl)ation on early gene expression induced by the microbe-associate molecular patterns (MAMPs) flagellin (flg22) and EF-Tu (elf18). Stringent statistical analyses and filtering identified 178 genes having MAMP-induced mRNA abundance patterns that were altered ...[more]
Project description:Transcriptional profiling of Arabidopsis thaliana seedlings comparing overexpressor with wild type, and knockout with wild type separately under control and NaCl stress. Overall design: Two-condition experiment, STOP1 overexpressor vs. Wild type (Col-0) and STOP1 knockout vs. Wild type (Col-0) seedlings under control and NaCl. Biological replicates: 3 overexpressor/knockout, 3 wild type (Col-0).
Project description:This study evaluates the transcriptome of Arabidopsis thaliana seedlings chronically exposed to the hormone Methyl Jasmonate (MeJA) or to the bacterial elicitor flg22 (a 22-amino acid peptide from flagellin). Treatments were performed under high and low phosphate availability using wild-type Col-0 plants and the phr1 phl1 mutant. Overall design: Arabidopsis seeds (wild-type Col-0 and the phr1 phl1 mutant) were germinated on Johnson medium (1 % sucrose) containing 1 mM Pi (in the form of KH2PO4) for 7 days in the vertical position and then transferred to 1 mM Pi and 5 µM Pi media containing 1 % sucrose either alone or supplemented with 10 µM MeJA or 1 µM flg22. Whole seedlings were harvested 12 days after the transferring. Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night). The experiment includes a total of six biological replicates from two independent experiments per condition.
Project description:Arabidopsis lines expressing 35S::Strep-SUMO1H89R in Col-0 background were generated since the H89R SUMO1 variant simplifies MS/MS detection of SUMO conjugated lysines after trypsinization (Miller et al., 2010). Transgenic seedlings were treated with water or 250nM flg22 for 30 minutes and total protein extracts including membrane fractions were affinity purified with Pierce™ Streptavidin Magnetic Beads. LC-MS analysis of eluting proteins allowed identification of candidate SUMO-conjugated proteins in response to flg22 treatment.
Project description:Gene Expression profiling of the Arabidopsis thaliana MAP Kinase Kinases 1 (mkk1), MAP Kinase Kinases 2 (mkk2) knockout mutants and the double mutant mkk1/mkk2 before and 24 hours after treatment with the salicylic acid analog BTH, was measured by hybridisation to an Affymetrix ATH1 GeneChip. Keywords: Gene expression. Combined mutant and treatment study Overall design: Whole Arabidopsis thaliana mkk1, mkk2 and mkk1/mkk2 knockout mutants and wild type plants (Col-0) were sampled in triplicates before and 24 hours after BTH treatment.
Project description:Gene Expression profiling of the Arabidopsis thaliana MAP Kinase Kinases 1 (mkk1), MAP Kinase Kinases 2 (mkk2) knockout mutants and the double mutant mkk1/mkk2 before and 24 hours after treatment with the salicylic acid analog BTH, was measured by hybridisation to an Affymetrix ATH1 GeneChip. Experiment Overall Design: Whole Arabidopsis thaliana mkk1, mkk2 and mkk1/mkk2 knockout mutants and wild type plants (Col-0) were sampled in triplicates before and 24 hours after BTH treatment.
Project description:a2e_heterosis - cgh_colvsc24_chr4 - Arabidopsis thaliana accessions (Col-0, C24 and Cvi) and their hybrid were used to investigate the dynamics of the epigenome after intraspecific hybridization between - Comparative genome hybridization between Arabidopsis thaliana accessions Col-0 and C24 Keywords: cgh,chip-chip Overall design: 2 dye-swap - Tiling arrays Chromosome IV Arabidopsis