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INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana.

ABSTRACT: INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana.

PROVIDER: PRJNA491484 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7865800_1.fastq.gz	Fastqsanger.gz
	SRR7865800_2.fastq.gz	Fastqsanger.gz
	SRR7865810_1.fastq.gz	Fastqsanger.gz
	SRR7865810_2.fastq.gz	Fastqsanger.gz
	SRR7865820_1.fastq.gz	Fastqsanger.gz

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INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana.

Project description:INDETERMINATE DOMAIN (IDD)/ BIRD proteins are a highly conserved plant-specific family of transcription factors which play multiple roles in plant development and physiology. Here, we show that mutation in IDD4/IMPERIAL EAGLE increases resistance to the hemi-biotrophic pathogen Pseudomonas syringae, indicating that IDD4 may act as a repressor of basal immune response and PAMP-triggered immunity. Furthermore, the idd4 mutant exhibits enhanced plant-growth indicating IDD4 as suppressor of growth and development. Transcriptome comparison of idd4 mutants and IDD4ox lines aligned to genome-wide IDD4 DNA-binding studies revealed major target genes related to defense and developmental-biological processes. IDD4 is a phospho-protein that interacts and becomes phosphorylated on two conserved sites by the MAP kinase MPK6. DNA-binding studies of IDD4 after flg22 treatment and with IDD4 phosphosite mutants show enhanced binding affinity to ID1 motif-containing promoters and its function as a transcriptional regulator. In contrast to the IDD4-phospho-dead mutant, the IDD4 phospho-mimicking mutant shows altered susceptibility to PstDC3000, salicylic acid levels and transcriptome reprogramming. In summary, we found that IDD4 regulates various hormonal pathways thereby coordinating growth and development with basal immunity.

| S-EPMC6345439 | biostudies-literature

INDETERMINATE-DOMAIN 4 (IDD4) coordinates immune responses with plant-growth in Arabidopsis thaliana.

Project description:We report the transcriptome composition of idd mutant with and without flg22 treatment compared to WT (ColO). Furthermore, we provide transcriptome data of a IDD4ox line and IDD4-phospho-peptide modified versions without treatment compared to WT (ColO), respectively. In order to identify the genomic regions targeted by IDD4 in vivo, Chromatin-Immunoprecipitation (ChIP) was performed followed by deep sequencing on the Illumina High-Sequencing2000 platform (SEQ).

2018-12-09 | GSE120068 | GEO

Salinity stress-induced phosphorylation of INDETERMINATE-DOMAIN 4 (IDD4) regulates plant growth adaptation in Arabidopsis

Project description:Salinity stress-induced phosphorylation of INDETERMINATE-DOMAIN 4 (IDD4) regulates plant growth adaptation in Arabidopsis

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INDETERMINATE DOMAIN-DELLA protein interactions orchestrate gibberellin-mediated cell elongation in wheat and barley

Project description:INDETERMINATE DOMAIN-DELLA protein interactions orchestrate gibberellin-mediated cell elongation in wheat and barley

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Preoperative Diagnosis of Benign Thyroid Nodules with Indeterminate Cytology

Project description:BACKGROUND: Following fine needle aspiration, 15-30% of thyroid nodules are not clearly benign or malignant. These cytologically indeterminate nodules are often referred for diagnostic surgery, though most prove benign. A novel diagnostic test measuring the expression of 167 genes has shown promise in improving pre-operative risk assessment. We evaluated this test in a prospective, multicenter study. METHODS: Over 19 months, we performed a prospective study at 49 clinical sites enrolling 3,789 patients and collecting 4,812 samples from thyroid nodules >1cm requiring evaluation. We obtained 577 cytologically indeterminate aspirates with corresponding histopathology of excised lesions on 413. Central blinded histopathologic review served as the reference (“gold”) standard. After applying inclusion criteria, gene expression classifier results were obtained for 265 indeterminate nodules used in this analysis, and performance was calculated. RESULTS: 85 of 265 indeterminate nodules were malignant. The gene expression classifier correctly identified 78 of 85 as ‘suspicious’ (92% sensitivity, [84%-97%] 95% CI). Specificity was 52%, [44%-59%]. The negative predictive value was 95%, 94%, and 85%, respectively, for aspirates with AUS/FLUS, FN/SFN, or ‘suspicious’ cytology. Analysis of 7 false negative cases revealed 6 with a paucity of thyroid follicular cells, suggesting that insufficient sampling of the nodule had occurred. CONCLUSIONS: Though individualized clinical care is recommended, these data support consideration of a conservative approach for most patients with indeterminate FNA cytology and benign gene expression classifier results. 265 cytologically indetermine samples, 47 cytologically benign and 55 cytologically malignant samples

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Leaf margins of indeterminate Arabidopsis leaves

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INDETERMINATE DOMAIN-DELLA protein interactions orchestrate gibberellin-mediated cell elongation in wheat and barley

Project description:DELLA proteins are members of the GRAS-domain family of transcriptional regulators and modulate transcriptional activity through protein-protein interactions with at least 15 different classes of transcription factor. The plant hormone gibberellin (GA) regulates a range of growth and development responses including promoting cell elongation, by triggering the degradation of DELLA proteins. More than 70% of modern wheat (Triticum aestivum L.) varieties carry alleles encoding DELLA proteins that are resistant to GA-mediated degradation. These alleles result in constitutive growth repression in stem tissues and confer a semi-dwarf growth habit associated with improved lodging resistance. However, these alleles also have negative pleiotropic effects such as reduced nitrogen use efficiency and weak early vigour that restrict their utility in some environments. A detailed understanding of the mechanisms by which DELLA proteins regulate growth and development will be necessary to dissect these responses and develop targeted strategies to breed improved crop varieties. We identified the orthologous C2H2 Zinc-finger transcription factors INDETERMINATE DOMAIN 5 (IDD5) in wheat and SEMI-DWARF3 (SDW3) in barley (Hordeum vulgare) as positive regulators of stem and leaf expansion. Both IDD5 and SDW3 physically interact with DELLA proteins and are epistatic to these genes. We propose a mechanism by which IDD proteins integrate GA signals to modulate downstream gene transcriptional activity through a protein complex dual activation and repression activities. Changes in GA biosynthesis gene expression levels suggest that part of this response involves GA homeostasis. Plants carrying null mutations in IDD5 and SDW3 exhibit a GA-insensitive semi-dwarf growth habit comparable to the Rht-D1b ‘Green Revolution’ allele and have potential as novel dwarfing alleles in cereal breeding programmes.

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Salinity stress-induced phosphorylation of INDETERMINATE-DOMAIN 4 (IDD4) regulates plant growth adaptation in Arabidopsis

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