Early N-hydroxy-pipecolic acid transcriptional profile
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1096619 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28564027_1.fastq.gz | Fastqsanger.gz | |||
| SRR28564027_2.fastq.gz | Fastqsanger.gz | |||
| SRR28564028_1.fastq.gz | Fastqsanger.gz | |||
| SRR28564028_2.fastq.gz | Fastqsanger.gz | |||
| SRR28564029_1.fastq.gz | Fastqsanger.gz |
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Project description:N-hydroxy-pipecolic acid (NHP) is a mobile metabolite essential for inducing and amplifying systemic acquired resistance (SAR) following pathogen attack. In Arabidopsis thaliana (Arabidopsis), exogenous NHP is sufficient to activate SAR-related immune responses, including salicylic acid (SA) accumulation and changes in global transcriptional profile. Previous studies have tracked these changes 1-2 days after an initial NHP treatment, resulting in little knowledge of the very early phases of NHP signaling and transcriptional responses leading to immunity. Here we show NHP elicits transcriptional changes within minutes of treatment. We report distinct waves of expression over the course of minutes to hours defined by transient induction of jasmonic acid/wound-related responses, a primary induction of WRKY transcription factor expression, and subsequent induction of WRKY-regulated defense genes. The upregulation of WRKYs and the majority of defense-related genes occurred in the sid2-2 mutant, which is unable to accumulate SA upon NHP treatment, suggesting NHP is sufficient to drive the early phase of transcriptional changes in a low SA environment. We also show that WRKY70 is required for the expression of a set of genes defining the secondary transcriptional changes, as well as NHP enhancement of ROS production and SAR.
2024-08-16 | GSE263276 | GEO
Project description:The trade-off between growth and defense is a critical aspect of plant immunity. Therefore, the plant immune response needs to be tightly regulated. Salicylic acid (SA) is an important plant hormone regulating defense against biotrophic pathogens. Recently, N-hydroxy-pipecolic acid (NHP) was identified as anotherregulator for plant innate immunity and systemic acquired resistance. Although the biosynthetic pathway leading to NHP formation has already been identified, how NHP is further metabolized was unclear. Here, we present UGT76B1 as a UDP-dependent glycosyltransferase that modifies NHP by catalyzing the formation of 1-O-glucosyl-pipecolic acid (NHP-OGlc) in Arabidopsis thaliana. Analysis of T-DNA and CRISPR knock-out mutant lines of UGT76B1 by targeted and non-targeted UHPLC-HRMS underlined NHP and SA as endogenous substrates of this enzyme in response to Pseudomonas infection and UV treatment. ugt76b1 mutant plants have a dwarf phenotype and constitutive defense response which can be suppressed by loss of function of the NHP biosynthetic enzyme Flavin-dependent monooxygenase 1 (FMO1). This suggests that elevated accumulation of NHP contributes to the enhanced disease resistance in ugt76b1. Externally applied NHP can move to distal tissue in ugt76b1 mutant plants. Although glycosylation is not required for the long-distance movement of NHP during systemic acquired resistance, it is crucial to balance growth and defense.
2022-02-28 | MTBLS2334 | MetaboLights
Project description:Our aim is to explore the effect of Hydroxy-carboxylic Acid Receptor 1 on cardiomyocytes. Neonatal rat cardiomyocytes (NRCMs) were isolated and cultured. Subsequently, NRCMs were treated with the agonist of Hydroxy-carboxylic Acid Receptor 1 (HCAR1), 3Cl-HBA at 40 μM for 48 h(HBA1,HBA2 and HBA3) or DMSO as control(C1,C3 and C3). RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland), and was analysed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for quality control. The libraries were sequenced on an Illumina HiSeq X Ten platform. DESeq2 was used to analyse RNA-seq data. Neonatal rat cardiomyocytes (NRCMs) were isolated and cultured. Subsequently, NRCMs were treated with the agonist of Hydroxy-carboxylic Acid Receptor 1 (HCAR1), 3Cl-HBA (40 μM for 48 h) or DMSO as control. RNA was extracted using the KAPA RiboErase RNA-Seq kit (Roche, Basel, Switzerland), and was analysed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA) for quality control. The libraries were sequenced on an Illumina HiSeq X Ten platform.
2024-02-14 | GSE224822 | GEO
Project description:The Gram-positive soil bacterium Corynebacterium glutamicum is widely used in industrial fermentative processes for the production of amino acids. The world production of L-lysine has surpassed 2 million tons per year. Glucose is taken up into the C. glutamicum cell by the phosphotransferase system PTS which can be replaced and/or enhanced by a permease and a glucokinase. Heterologous expression of the gene for the high-affinity glucose permease from Streptomyces coelicolor and of the Bacillus subitilis glucokinase gene fully compensated for the absence of the PTS in ï??hpr strains and strains grew as fast with glucose as C. glutamicum wild type. Growth of PTS-positive strains with glucose was accelerated when the endogenous inositol permease IolT2 and the glucokinase from Bacillus subtilis were overproduced using plasmid pEKEx3-IolTBest. When the genome-reduced C. glutamicum strain GRLys1 carrying additional in-frame deletions of sugR and ldhA to derepress glycolytic and PTS genes and to circumvent formation of L-lactate as by-product was transformed with this plasmid, a 40% higher L-lysine titer and a 30% higher volumetric productivity as compared to GRLys1(pEKEx3) resulted. The non-proteinogenic amino acid pipecolic acid (L-PA), a precursor of immunosuppressants, peptide antibiotics or piperidine alkaloids, can be derived from L-lysine. To enable production of L-PA by the L-lysine producing strain, the L-Lysine dehydrogenase gene lysDH from Silicibacter pomeroyi and the endogenous pyrroline 5-carboxylate reductase gene proC were expressed as synthetic operon. This enabled C. glutamicum to L-PA with a yield of 0.49 ± 0.03 gg-1 and a volumetric productivity of 0.04 ± 0.00 gL-1h-1.To the best of our knowledge, this is the first fermentative process for the production of L-PA. Two conditions tested, 200 mM NaCl Vs 200 mM pipecolic supplemented in the culture medium, control experiments done with the addition of 200mM of NaCl. Four technical replicates.
2016-03-30 | E-GEOD-79690 | biostudies-arrayexpress
Project description:Exercise is usually regarded to have short-term beneficial effects on immune health. Here we show that early-life regular exercise exerts long-term beneficial effects on inflammatory immunity. Swimming training for 3 months in male mice starting from 1-month-old curbed cytokine response and mitigated sepsis when exposed to lipopolysaccharide (LPS) challenge, even after 11-month interval of detraining. Metabolomics analysis of serum and liver identified pipecolic acid (a non-encoded amino acid) as a pivotal metabolite responding to early-life regular exercise. We then explored histone epigenetic modifications and observed a significant increase of H3K4me3 expression in the liver of 15-month-old mice exposed to early-life exercise. To further unravel the prolonged increased pipecplic acid production raised by early-life exercise, we conducted ChIP-seq analysis and found H3K4me3 occupancy at Crym (a key enzyme responsible for catalyzing pipecolic acid production) promoter has a significant increase in hepatocytes of early-life exercised mice. Our findings demonstrate that early-life regular exercise enhances anti-inflammatory immunity during middle-aged phase in male mice via epigenetic immunometabolic modulation, in which hepatic pipecolic acid production plays a pivotal role.
2024-03-12 | GSE255161 | GEO
Project description:Transcriptional response of Arabidopsis thaliana to exogenous application of pipecolic acid
| PRJEB23627 | ENA
Project description:Pipecolic acid or L-PA is a cyclic amino acid derived from L-lysine which has gained interest in the recent years within the pharmaceutical and chemical industries. L-PA can be produced efficiently using recombinant Corynebacterium glutamicum strains by expanding the natural L-lysine biosynthetic pathway. We show that de novo synthesized or externally added L-PA partially is beneficial for growth under hyper-osmotic stress conditions. C. glutamicum cells accumulated L-PA under elevated osmotic pressure and released it after an osmotic down shock. The proline permease ProP was identified as a candidate L-PA uptake system since RNAseq analysis revealed increased proP RNA levels upon L-PA production
2019-05-31 | GSE122249 | GEO
Project description:The protein kinase OXI1 is induced by a large number of stress conditions and regulates the interaction of plants with pathogenic and beneficial microbes but little is yet known on the underlying mechanisms. In this work, we generated Arabidopsis OXI1 knock out and overexpression lines and show by transcriptome, proteome and metabolome analysis. Our work revealed that OXI1 regulates biosynthesis of SA via CBP60g-induced expression of isochorismate synthase SID2. OXI1 also induces the transcription factor WRKY33 and its downstream target PAD3, resulting in accumulation of camalexin. Moreover, OXI1 regulates ALD1, SARD4 and FMO1 to promote the biosynthesis of pipecolic acid (Pip) and N-hydroxy pipecolic acid (NHP), mediating systemic acquired resistance to bacterial infection. In contrast to OXI1 overexpressor plants, OXI1 knock out plants show enhanced expression of nuclear and chloroplast genes of photosynthesis, and accordingly enhanced growth under ambient conditions. Overall, these results show that OXI1 plays a key role in regulating the trade-off between growth and defense in plants.
2022-11-22 | PXD023853 | Pride
Project description:Activation of Hydroxy-carboxylic Acid Receptor 1 effect on cardiomyocytes
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Project description:Transcriptional response of Arabidopsis thaliana in systemic acquired resistance: critical roles for pipecolic acid and salicylic acid
| PRJEB12204 | ENA