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Transcriptome analysis of Arabidopsis low molecular weight protein phosphatase mutant aph in response to Abscisic acid

ABSTRACT: We compared the the transcriptome of wild type and a knock-out mutant of Involvement of low molecular weight protein tyrosine phosphatase, aph-1, with or without ABA treatment in Arabidopsis

ORGANISM(S): Arabidopsis

PROVIDER: GSE186664 | GEO | 2021/10/29

REPOSITORIES: GEO

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Involvement of low molecular weight tyrosine acid phosphatase in abscisic acid signaling in Arabidopsis

Project description:Low molecular weight protein tyrosine phosphatase (LWM-PTP) is highly conserved tyrosine phosphatase from plants to animals. The function and putative targets of plant LWM-PTP homolog is not reported yet. Here, we revealed that Arabidopsis LWM-PTP homolog APH is a functional tyrosine phosphatase. APH participates in ABA signaling and regulates the ABA-responsive genes by regulates the tyrosine phosphorylation of multiple splicing factors and other transcriptional regulators. APH may also target RAF9, a member of B2 and B3 RAF kinases that activates SnRK2s, the key components in ABA-receptor coupled core signaling pathway. We preformed genetic analysis and found the aph mutants are hyposensitive to ABA in post-germination growth. We also performed an anti-phosphotyrosine antibody-based phosphoproteomics and studied the global change of phosphotyrosine in response to the ABA and APH. Hundreds of proteins, include SR45 and RAF9, are identified putative targets of APH. Consistent with it, aph mutants showed an ABA hyposensitive phenotype and altered expression of ABA-highly-responsive genes. Our results reveal a crucial function of APH in regulating tyrosine phosphorylation and ABA signaling in model plant Arabidopsis.

2022-10-14 | PXD029650 | Pride

Transcriptome analysis of Arabidopsis low molecular weight protein phosphatase mutant aph in response to Abscisic acid

Project description:Transcriptome analysis of Arabidopsis low molecular weight protein phosphatase mutant aph in response to Abscisic acid

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Arabidopsis NRP switches off the PP6 phosphatase FyPP3 to repress auxin-mediated growth in response to abscisic acid

Project description:How environmentally challenged plants can switch from growth to stress adaptation is an important question in plant physiology. To identify the key regulatory proteins and to characterize the underlying signaling pathways are essential in answering this question. Here we show that the abiotic stress hormone Abscisic acid (ABA) induces the expression of the Asparagine rich proteins (NRP), DCD1 and DCD2, to repress the auxin-induced growth by promoting vacuolar degradation of PIN2, the auxin efflux carrier. ABA-induced degradation of PIN2 is inhibited in the dcd1 dcd2 double mutant, and inhibition of FyPP3, the catalytic subunit of the PP6 protein phosphatase, can restore the PIN recycling and growth phenotype in the double mutant. Transcriptome analyses on WT, dcd1 dcd2, the FyPP3 Dominant Negative line (FyPP3-DN), and dcd1 dcd2/FyPP3-DN supported the essential function of the NRP-FyPP3 module in the growth- to stress-response switch.

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PTP4A1 phosphatase is overexpressed in systemic sclerosis fibroblasts and promotes TGFb signaling

Project description:We show that silencing of tyrosine phosphatase PTP4A1 attenuates pro-fibrotic TGFb signaling in human dermal fibroblasts

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PEST-domain-enriched tyrosine phosphatase and glucocorticoids as regulators of mast cell signalling

Project description:PEST-domain-enriched tyrosine phosphatase (PEP) is a cytoplasmic protein tyrosine phosphatase that regulates immune cell functions, including mast cell functions. Using bone marrow derived mast cells (BMMCs) from PEP+/+ and PEP-/- mice, RNA-seq data showed that dinitrophenol (DNP) - activated PEP-/- BMMCs have misregulated gene expression, with some cytokine/chemokine genes (eg.TNFα, IL13, CSF2) showing reduced gene expression in the dinitrophenol (DNP) - activated PEP-/- BMMCs compared to (DNP)-activated PEP+/+ BMMCs. Also, the ability of the glucocorticoid dexamethasone (Dex) to negatively regulate DNP - induced COX-2 gene expression in PEP-/- BMMCs was inhibited compared to the PEP+/+ BMMCs.

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Transcription profiling of Drosophila tissue expressing phosphatase mutant eya shows that reducing phosphatase activity did not globally impair transcriptional output

Project description:Drosophila eye specification an development relies on a collection of transcription factors termed the retinal determination gene network (RDGN). Two members of this network, Eyes absent (EYA) and Sine oculis (SO), form a transcriptional complex in which EYA provides the transactivation function while SO provides the DNA binding activity. EYA also function as a protein tyrosine phosphatase, raising the question of whether transcriptional output is dependent or independent of phosphatase activity. To explore this, we used microarrays together with binding site analysis, quantitative real-time PCR, chromatin immunoprecipitation, genetics, and in vivo expression analysis to identify new EYA-SO targets. In parallel, we examined the expression profiles of tissue expressing phosphatase mutant eya and found that reducing phosphatase activity did not globally impair transcriptional output. Among the targets identified by our analysis was the cell cycle regulatory gene, string (stg), suggesting that EYA and SO may influence cell proliferation through transcriptional regulation of stg. Future investigation into the regulation of stg and other EYA-SO targets identified in this study will help elucidate the transcriptional circuitries whereby output from the RDGN integrates with other signaling inputs to coordinate retinal development. Experiment Overall Design: We compared gene expression across duplicate samples for controls in which eya was not overexpressed to duplicate samples in which a wildtye overexpressed eya transgene, an eya mutant transgene with the D493N mutation, which reduces phosphatase activity, and a second eya mutant transgene with the E728Q mutation, which has little is any posphatase activity.

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The purine metabolite allantoin enhances abiotic stress tolerance through synergistic activation of abscisic acid metabolism

Project description:Purine catabolism is regarded as a housekeeping function that remobilizes nitrogen for plant growth and development. However, emerging evidence suggests that certain purine metabolites might contribute to stress protection of plants. Here, we show that in Arabidopsis, the intermediary metabolite allantoin plays a role in abiotic stress tolerance via activation of abscisic acid (ABA) metabolism. The aln loss-of-function of ALN, encoding allantoinase, results in increased allantoin accumulation, genome-wide up-regulation of stress-related genes, and enhanced tolerance to drought-shock and osmotic stress in aln mutant seedlings. This phenotype is not caused by a general response to purine catabolism inhibition, but rather results from a specific effect of allantoin. Allantoin activates ABA production both through increased transcription of NCED3, encoding a key enzyme in ABA biosynthesis, and through post-translational activation via high-molecular-weight complex formation of BG1, a ß-glucosidase hydrolyzing glucose-conjugated ABA. Exogenous application of allantoin to wild-type plants also activates the two ABA-producing pathways that lead to ABA accumulation and stress-responsive gene expression, but this effect is abrogated in ABA-deficient and BG1-knockout mutants. We propose that purine catabolism functions not only in nitrogen metabolism, but also in stress tolerance by influencing ABA production, which is mediated by the possible regulatory action of allantoin.

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Subcutaneous adipose tissue: comparison of weight maintainence and weight regain following an 8-week low calorie diet

2011-09-30 | GSE24432 | GEO

Subcutaneous adipose tissue: comparison of weight maintainence and weight regain following an 8-week low calorie diet

Project description:The present study was designed to identify determinants that foreshadow successful weight maintenance. More specifically, we examined whether subcutaneous adipose tissue (scAT) gene expression of participants who experience successful weight maintenance following caloric restriction differed from that of participants who regain weight. Forty women followed a dietary protocol consisting of an 8-week low calorie diet (LCD) and a 6-month weight maintenance phase. At the end of the protocol, participants were classified as weight maintainers (WM; 0-10% weight regain) and weight regainers (WR; 50-100% weight regain). Anthropometric measurements, plasma parameters, and scAT biopsies were taken before and after the LCD. Adipose tissue gene expression profiles were studied in all individuals before and after the LCD.

2011-09-29 | E-GEOD-24432 | biostudies-arrayexpress

Protein Tyrosine Phosphatase UBASH3B is Overexpressed in Triple-Negative Breast Cancer and Promotes Invasion and Metastasis

Project description:Efforts to improve the clinical outcome of highly aggressive triplenegative breast cancer (TNBC) have been hindered by the lack of effective targeted therapies. Hence, it is important to identify the specific gene targets/pathways driving the invasive phenotype to develop more effective therapeutics. Here we show that UBASH3B (ubiquitin associated and SH3 domain containing B), a protein tyrosine phosphatase, is overexpressed in TNBC, where it supports malignant growth, invasion and metastasis in large through modulating EGFR. We also show that UBASH3B is a functional target of anti-invasive miR-200a that is downregulated in TNBC. Importantly, the oncogenic potential of UBASH3B is dependent on its tyrosine phosphatase activity, which targets CBL ubiquitin ligase for dephosphorylation and inactivation, leading to EGFR upregulation. Thus, UBASH3B may function as a crucial node in bridging multiple invasion-promoting pathways, thus providing a potential new therapeutic target for TNBC. Breast cancer tissues and breast cancer cell lines

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