Transcriptional response of Arabidopsis thaliana to exogenous application of N-hydroxypipecolic acid (NHP).
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ABSTRACT:
PROVIDER: PRJEB43717 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5489950.fastq.gz | Fastqsanger.gz | |||
| ERR5489960.fastq.gz | Fastqsanger.gz | |||
| ERR5489951.fastq.gz | Fastqsanger.gz | |||
| ERR5489961.fastq.gz | Fastqsanger.gz | |||
| ERR5489952.fastq.gz | Fastqsanger.gz |
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Project description:Previous studies from our laboratory have shown that the resistance increase observed after biological systemic acquired resistance (SAR) induction in plants can be mimicked by exogenous plant treatment with N-hydroxypipecolic acid (NHP, Hartmann et al., 2018, Schnake et al., 2020). Moreover, exogenous application of the NHP biosynthetic precursor pipecolic acid (Pip) induced a transcriptional response that was overlapping with the SAR transcriptional response and fully depended on the NHP synthase FMO1 (Hartmann et al., 2018; E-MTAB-6243). In order to investigate whether elevations of NHP lead to a SAR-like transcriptional reprogramming, we supplied individual Arabidopsis wildtype Col-0 plants, as well as sid2-1 and npr1-3 mutant plants, with doses of 10 µmol NHP and determined the transcriptional response in leaves 24 hours later on the whole genome level by RNA-sequencing analyses in relation to control-treated (H2O) plants. Col-0 plants were additionally treated with doses of 10 µmol Pip in order to directly compare the transcriptional responses of the foliage between Pip and NHP. Arabidopsis thaliana plants were grown individually in pots containing a mixture of soil, vermiculite and sand (8:1:1) in a controlled cultivation chamber with a 10-h day (9 AM to 7 PM; photon flux density 100 mol m-2 s-1) / 14-h night cycle and a relative humidity of 70 %. Day and night temperatures were set to 21°C and 18°C, respectively. Experiments were performed with 5-week-old, naive plants exhibiting a uniform appearance. Treatments with NHP and Pip were essentially performed as detailed in Hartmann et al. (2018, Cell 173, 456–469). In brief, 10 ml of a 1 mM aqueous solution of NHP or Pip (equates to a dose of 10 µmol) were pipetted onto the soil of individually cultivated plants. 10 ml of water applied in the way served as control treatments. In total, three biologically independent, replicate experiments were performed. In each experiment, 18 full-grown leaves from 6 different plants were pooled 24 hours after the respective treatments for one biological replicate. In this way, 3 biologically independent, replicate samples per treatment and plant genotype were obtained.
2021-05-03 | E-MTAB-10230 | biostudies-arrayexpress
Project description:Transcriptional response of Arabidopsis thaliana to exogenous application of pipecolic acid
| PRJEB23627 | ENA
Project description:We have previously shown that the resistance increase observed after biological systemic acquired resistance (SAR) induction in plants can be mimicked by exogenous plant treatment with (pipecolic acid) Pip (Návarová et al., 2012; Bernsdorff et al., 2016). In order to investigate whether elevations of Pip are sufficient for a SAR-like transcriptional reprogramming in leaf tissue, we supplied individual Arabidopsis Col-0 and fmo1 mutant plants with doses of 10 µmol Pip and determined the transcriptional response in leaves one day later on the whole genome level by RNA-sequencing analyses in relation to untreated plants. Arabidopsis thaliana plants were grown individually in pots containing a mixture of soil, vermiculite and sand (8:1:1) in a controlled cultivation chamber with a 10-h day (9 AM to 7 PM; photon flux density 100 mol m-2 s-1) / 14-h night cycle and a relative humidity of 70 %. Day and night temperatures were set to 21°C and 18°C, respectively. Experiments were performed with 5- to 6-week-old, naive plants exhibiting a uniform appearance.Treatments with Pip were essentially performed as detailed in Návarová et al. (2012).10 ml of a 1 mM aqueous solution of Pip (equates to 10 µmol) were pipetted onto the soil of individually cultivated plants. 10 ml of water were applied in the control treatments. Three biologically independent, replicate experiments were performed. In each experiment, at least 4 full-grown leaves from 6 different plants were pooled 24 hours after the treatment with Pip or water for one biological replicate. In this way, 3 biologically independent, replicate samples per treatment and plant genotype were obtained.
2018-03-23 | E-MTAB-6243 | biostudies-arrayexpress
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:bacterium NHP-B Genome sequencing and assembly
| PRJNA507068 | ENA
Project description:Transcriptional response of Arabidopsis thaliana to exogenous application of pipecolic acid
2018-06-04 | E-MTAB-6243 | ExpressionAtlas
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| PRJEB30670 | ENA
Project description:Normal human prostate (NHP) epithelial cells undergo senescence in vitro and in vivo, but the underlying molecular mechanisms remain incompletely understood. Here we first show that multiple primary strains of NHP cells are all immunophenotyped as CK5+/CK18+CD44+α2β1+p63+hTERT+ progenitor cells, which gradually lose progenitor markers as they lose proliferative capacity. NHP cell senescence involves loss of telomerase expression, upregulation of p16, and activation of p53. Using genetically defined manipulations of these three signaling pathways, we show that p16 is the primary determinant of the NHP cell proliferative capacity and hTERT is required for unlimited proliferative lifespan. Hence, suppression of 16 alone significantly extends NHP cell lifespan but both p16 inhibition and hTERT are required to immortalize NHP cells. Importantly, the immortalized NHP cells are normal progenitors that possess the ability to differentiate into functional prostatic glands containing both basal and luminal cells and, frequently, neuroendocrine cells. The immortalized NHP cells possess gene expression profiles characteristic of proliferating progenitor cells. Our studies shed light on the molecular mechanisms regulating the proliferative lifespan of NHP progenitor cells and provide direct evidence that basal-like progenitor cells can regenerate the entire prostatic glands in vivo. The availability of these cells should facilitate future studies of prostate cancer development. Further processed data linked below as Supplementary files. TestvsControl: corresponding GSM# 3vs1: GSM266720, 721, 722 4vs1: GSM266727, 730, 731 5vs1: GSM266732, 733, 734 7avs1: GSM266735, 736, 737 9vs1: GSM266772, 773, 812 11vs1: GSM266813, 816, 823 13vs1: GSM266824, 826, 828 Note: The 'TestvsControl' comparisons report the top 100 up- or down-regulated genes. The numeric designations (1 to 13) are used in the corresponding manuscript. The 'SignificantGenes' lists were used in clustering analysis. Keywords: Cell type comparison (senscent and immortalized NHP cells compared to young NHP progenitors)
2008-10-09 | GSE10570 | GEO
Project description:Effect of Exogenous Retinoic Acid on human iPSCs derived intestinal organoids
| PRJNA875061 | ENA
Project description:This study evaluates the effects of exogenous auxin on the Arabidopsis thaliana root proteome at 8, 12, and 24 hours post-treatment.
2017-07-18 | PXD001400 | Pride