E-GEOD-10646
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA107725
PROVIDER: E-GEOD-10646 | ExpressionAtlas | 2014-07-03
REPOSITORIES: ExpressionAtlas
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Project description:Zhou2015 - Circadian clock with immune
regulator NPR1
Arabidopsis clock model modified from
P2012 (Pokhilko et al., 2013 -
BIOMD0000000445)
model to include the master immune regulator NPR1 coupling to LHY,
TOC1 and PRR7.
Triggers: The Global Quantities contain triggers that allow
one to change coupling settings, Salicyclic acid (SA) treatment and
npr1 mutants.
LHY_on: true->NPR1 couples to LHY
PRR7_on: true->NPR1 couples to PRR7
WT: true->WT plants, false->npr1 mutant plants
SA: true->SA treated plants, false->no treatment
This model has L=1, i.e. operates only under constant light
conditions and is not aiming to make preditions under diurnal
conditions. Due to period overshoot only time points after 28h are
relevant.
This model is described in the article:
Redox rhythm reinforces the
circadian clock to gate immune response.
Zhou M, Wang W, Karapetyan S, Mwimba
M, Marqués J, Buchler NE, Dong X.
Nature 2015 Jun;
Abstract:
Recent studies have shown that in addition to the
transcriptional circadian clock, many organisms, including
Arabidopsis, have a circadian redox rhythm driven by the
organism's metabolic activities. It has been hypothesized that
the redox rhythm is linked to the circadian clock, but the
mechanism and the biological significance of this link have
only begun to be investigated. Here we report that the master
immune regulator NPR1 (non-expressor of pathogenesis-related
gene 1) of Arabidopsis is a sensor of the plant's redox state
and regulates transcription of core circadian clock genes even
in the absence of pathogen challenge. Surprisingly, acute
perturbation in the redox status triggered by the immune signal
salicylic acid does not compromise the circadian clock but
rather leads to its reinforcement. Mathematical modelling and
subsequent experiments show that NPR1 reinforces the circadian
clock without changing the period by regulating both the
morning and the evening clock genes. This balanced network
architecture helps plants gate their immune responses towards
the morning and minimize costs on growth at night. Our study
demonstrates how a sensitive redox rhythm interacts with a
robust circadian clock to ensure proper responsiveness to
environmental stimuli without compromising fitness of the
organism.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000577.
To cite BioModels Database, please use:
BioModels Database:
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-10 | BIOMD0000000577 | BioModels
Project description:Purpose: The experiment is to compare the NGS-derived seedling and leaf transcriptome profiling (RNAseq) of an Arabidopsis mutant ahl13 with that of wild type upon bacterial pathogen (pst DC3000) and flagellin elicitation. Method： The mRNA profiles of 10-day-old wild-type (WT) and AHL13 knockout (ahl13, SALK_014014) Arabidopsis were generated by RNAseq using Illumina NovaSeq6000. The sequence reads were passed through quality filters and mapped to Arabidopsis genome by TopHat2 followed by transcript splicing and quantitation by Cufflinks. DESeq was done to analyze differential gene expressions. qRT–PCR validation was performed using SYBR Green assays Result: We mapped about 20 million sequencing reads per sample to the Arabidopsis genome and identified approximately 28,000 transcripts in the Arabidopsis Col-0 and ahl13 mutant using TopHat2. Differentially expressed genes were identified using DESeq2 and about 166 genes show up-regulation in ahl13 upon DC3000 infection (FC>2, FDR<0.01) Conclusions: The ahl13 mutant exhibit differential transcription profile from that of Col-0 upon DC3000 treatment but similar upon flg22 treatment.
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