Unknown,Transcriptomics,Genomics,Proteomics

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INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and its receptors HAE/HSL2 are required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Reidunn Aalen

PROVIDER: E-GEOD-48108 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level. Arabidopsis thaliana (ecotype Colombia-0) seeds were grown in 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite), 3 plants per pot. Plants were kept in growth chambers VM-CM-6tsch VB 1514 (VM-CM-6tsch Industrietechnik GmbH, Germany) under the following conditions: a 8/16 h (light/dark) photoperiod at 22M-BM-0C/18M-BM-0C, 40%/70% relative humidity, and 70/0 M-NM-<mol m-2s-1 light intensity. After 32 days plants had 8 fully developed leaves. Each plant was infested with 32 wingless aphids [Brevicoryne Brassicae] (4 per leaf), which were transferred to leaves with a fine paintbrush. Infested plants and aphid-free controls were kept in plexiglass cylinders. Plants were harvested 72 h after infestation between the 6th and 8th hour of the light photoperiod. Four biological replicates were prepared from aphid infested and control plants, each sampled from 15 individual plants. Whole rosettes were cut at the hypocotyls and aphids were removed by washing with Milli-Q-filtered water. Differences in transcriptional responses were measured by comparing genes expression of aphid infested plants against non-infested control plants.

Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level. Arabidopsis thaliana (ecotype Colombia-0) seeds were sown into 6-cm-diameter pots filled with a sterile soil mix (1.0 part soil and 0.5 part horticultural perlite). Plants were kept in growth chambers VM-CM-6tsch VB 1514 (VM-CM-6tch Industrietechnik GmbH, Germany) with a 16/8 h (light/dark) photoperiod at 22/18 M-BM-0C, 40/70% relative humidity, and 70/0 mmol m-2 s-1 light intensity. The Pseudomonas syringae pv. tomato strain DC3000 culture was grown overnight in 10 ml of Kings B solution supplemented with antibiotics rifampicin (50 M-NM-<g mlM-bM-^HM-^R1) and kanamycin (25 M-NM-<g mlM-bM-^HM-^R1). Overnight culture was washed once in 10 mM MgCl2 and final cell densities were adjusted to approximately 0.20 at 600 nm (approximately 1.5 M-CM-^W 108 cfu mlM-bM-^HM-^R1) in 10 mM MgCl2. Plants were mock-challenged with 10 mM MgCl2 or inoculated with DC3000 strain, 3-4 leaves were infiltrated on the abaxial surface with a needleless 1-ml syringe.Whole rosettes were cut at the hypocotyls and harvested from Pseudomonas infested and mock-infected plants after 72 hours treatment. 4 biological replicates were prepared from each treatment, each containing rosettes from 15 individual plants. Differences in transcriptional responses were measured by comparing genes expression of Pseudomonas infected plants against mock-infected control plants.

Project description:Seed development is dependent on a well-orchestrated interplay between different transcriptional programs operating in the embryo, the endosperm and the maternally derived seed coat. In angiosperms, the embryo and the endosperm are products of double fertilization during which the two pollen sperm cells fuse with the egg cell and the central cell of the female gametophyte. In Arabidopsis, mutation of the cell cycle regulator CYCLIN DEPENDENT KINASE A;1 (CKDA;1) results in pollen that only successfully fertilizes the egg cell. Seeds generated from crosses with cdka;1 pollen develop endosperm with solely maternal and no paternal contribution. Here we have exploited cdka;1 fertilization as a novel tool for genomic dissection of parental effects during seed development. We have generated genome-wide transcription profiles of cdka;1 fertilized seeds. By this approach, we identified 11 differentially expressed AGAMOUS-LIKE (AGL) genes encoding Type-I MADS-box transcription factors. Here, AGL36 was chosen for an in-depth study. We show that AGL36 is imprinted and only expressed from the maternal genome. In addition, we demonstrate that AGL36 imprinting is controlled by the activity of METHYLTRANSFERASE1 (MET1) maintenance DNA methyltransferase and DEMETER (DME) DNA glycosylase. Interestingly, our data also show that the active maternal allele of AGL36 is regulated throughout endosperm development by components of the FIS Polycomb Repressive Complex 2 (PRC2). These findings shed novel light on the interplay between maternal and paternal genomes in the seed and how imprinting is coordinated by different mechanisms. 3 biological replicates, each consisting of 35 siliques from 10 individual plants, were used. Arabidopsis thaliana wild type (ecotype Colombia-0 and Ler-0) and cdka;1 mutant (At3g48750 /SALK_109806) were sown out on soil and grown under the following conditions: 18oC day and 18oC night, 16 hr day length with 30 min adjustment of light to on and off, and 85 Î¼mol/m2/sek in light intensity. For each replica, 10 Ler plants were emasculated and pollinated after 48 hours, either with individual WT Col or with individual cdka;1 mutant pollen. Three days after pollination (3 DAP), the siliques of each biological replicate were dissected with hypodermic needles to remove carpel walls, the pistil with pollen attached to it and the pedicel with abcsission zone. The remaining seeds attached to the middle lamella were harvested in bulk in liquid nitrogen at the same time of the day. Biological replicas are dye-swapped between slides.