Diacylglycerol Kinase 1 and Associated Lipid Mediators Modulate Rice Root Architecture
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE118455 | GEO | 2020/08/11
REPOSITORIES: GEO
Similar Datasets
Project description:Diacylglycerol Kinase 1 and Associated Lipid Mediators Modulate Rice Root Architecture
| PRJNA485702 | ENA
Project description:Ginsenoside 20(S)-Rg3, an active saponin monomer extracted from red ginseng, inhibits the malignancy of ovarian cancer cells. RNA-Seq analysis was used for deep sequencing of lncRNA to detected molecular mechanisms of 20(S)-Rg3.We identified 85 differentially expressed lncRNA influenced by 20(S)-Rg3, among which 67 lncRNAs were significantly decreased (fold change<0.5, p<0.05) including 12 ncRNAs and 55 pseudo genes, and 18 lncRNAs were significantly increased (fold change>1.5, p<0.05) including 3 ncRNAs, 14 pseudo genes and 1 unknown gene. This study provide a valuable resource for the discovery of lncRNAs related to anti-tumor mechanism of 20(S)-Rg3.
2021-02-16 | GSE118216 | GEO
Project description:To understand the effect of high and low GA levels on plant metabolism and development in Arabidopsis we made use of the GA biosynthesis inhibitor paclobutrazol (PBZ) and exogenously applied GA. The whole genome response at the translation level was assessed by immunopurification of polysomes from PBZ- and GA treated plants expressing FLAG-tagged ribosomal protein L18 (RPL18B). Polysomal associated RNA was isolated and subjected to affymterix ATH1 CHIP analysis. A total of 140 genes were statistically determined to be differentially translated after GA treatment whereas 89 genes where affected PBZ treatment. Our analysis revealed that GA and PBZ have opposing effects on the expression of cell wall and wax layer biosynthesis related genes. In addition, many genes involved in secondary metabolism are upregulated upon PBZ treatment. A set of SAUR-like genes important for mediating auxin responses are downregulated by PBZ, which is of interest to coordinatian of GA levels with growth and development. Interestingly, GA treatment induces the upregulation of transcription factors related to plant defense and senescence, which is in agreement with the early flowering upon GA treatment. Our study provides a first picture of the response of Arabidopsis to altered GA levels at the translation level, and thus will be valuable for understanding gene regulation at the polysome level. Two replicates for each treatment including GA, PBZ and control samples.
2011-06-03 | E-GEOD-29699 | biostudies-arrayexpress
Project description:To understand the effect of high and low GA levels on plant metabolism and development in Arabidopsis we made use of the GA biosynthesis inhibitor paclobutrazol (PBZ) and exogenously applied GA. The whole genome response at the translation level was assessed by immunopurification of polysomes from PBZ- and GA treated plants expressing FLAG-tagged ribosomal protein L18 (RPL18B). Polysomal associated RNA was isolated and subjected to affymterix ATH1 CHIP analysis. A total of 140 genes were statistically determined to be differentially translated after GA treatment whereas 89 genes where affected PBZ treatment. Our analysis revealed that GA and PBZ have opposing effects on the expression of cell wall and wax layer biosynthesis related genes. In addition, many genes involved in secondary metabolism are upregulated upon PBZ treatment. A set of SAUR-like genes important for mediating auxin responses are downregulated by PBZ, which is of interest to coordinatian of GA levels with growth and development. Interestingly, GA treatment induces the upregulation of transcription factors related to plant defense and senescence, which is in agreement with the early flowering upon GA treatment. Our study provides a first picture of the response of Arabidopsis to altered GA levels at the translation level, and thus will be valuable for understanding gene regulation at the polysome level.
2011-06-03 | GSE29699 | GEO
Project description:The angio-suppressive effect of 20(R)-ginsenoside Rg3 (Rg3-R) has been previously demonstrated, and microRNAs (miRNAs) are a vital group of small non-coding RNAs that function as post-transcriptional modulator of gene expression. Thus, using human umbilical vein endothelial cells (HUVEC) as model, we compared the microRNA (miRNA) expression profile of vascular endothelial growth factor (VEGF)-induced cells with the profile of the cell co-treated with VEGF and Rg3-R. Among the screened 553 human miRNAs, 6 up-regulated (miR-520h, miR-487b, miR-197, miR-524*, miR-342 and miR-219) and 3 down-regulated (miR-23a, miR-489 and miR-377) miRNAs were detected in Rg3-R treated vascular endothelial growth factor (VEGF)-induced HUVECs compared to VEGF alone. Real time RT-PCR was subsequently performed to verify the miRNA microarray result. Two condition experiment: VEGF-induced HUVEC and VEGF-induced HUVEC treated with Rg3-R. Three independent microarray experiments, with triplicate per microarray.
2011-09-09 | E-GEOD-31959 | biostudies-arrayexpress
Project description:RNA sequencing experiments revealed that the killing effect of the GO-Rg3-DOX nanoplatform proceeds primarily by downregulation of anti-apoptotic and angiogenesis related genes
2023-02-27 | GSE185139 | GEO
Project description:Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP) in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant.
2014-12-19 | GSE64290 | GEO
Project description:Background: Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine. Results: In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed. Conclusions: Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.
2020-07-20 | GSE153169 | GEO
Project description:The breast cancer incidence has been increasing in China, with the earlier age of onset compared with Western countries. Traditional Chinese medicine has been provided as one of the major source of anti-cancer drugs. Ginseng is one of the most common traditional medicines in China. Ginsenosides, the saponins in the plant Panax (ginseng) are the major active components responsible for their chemopreventive effects from cancer. However, the mechanisms by which ginsenosides exert their anti-cancer effect remain elusive. By combining TMT-based quantitation with TiO2-based phosphopeptide enrichment, we performed a quantitative analysis of the changes of the phosphoproteomes in ginsenoside Rg3-treated breast cancer MDA-MB-231 cells. We were able to quantitate 5,140 phosphorylation sites on 2,041 phosphoproteins. Our data show that the phosphorylation status of 13 sites was changed in MDA-MB-231 cells upon Rg3 treatment. The perturbed phosphoproteins are CPSF7, EEF2, HIRIP3, MAGED2, MPRIP, MYCBP2, PAWR, PPP1R12A, RANBP2, SEPT9, TMPO, and UFL1. These proteins are involved in various biological processes, including protein synthesis, cell division, and inhibition of NF-κB signaling. Our study revealed that Rg3 exerts its anti-cancer effects through a combination of different signaling pathways.
2018-01-08 | PXD003092 | Pride
Project description:Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). High temperature can induce earlier bolting which decreases in both quality and production of lettuce. However, knowledge underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems in the bolting period induced by high temperature (33 °C) compared with a control (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications. High temperature induced lettuce bolting, while control temperature did not. Of the 6656 proteins identified, 758 proteins significantly altered their expression level induced by high-temperature relative to the control, of which 409 were up-regulated and 349 down-regulated. Proteins with abundance level change were mainly involved in photosynthesis, carbohydrate metabolism, stress response, hormone synthesis, and signal transduction. These differential proteins were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involving in auxin (IAA) biosynthesis. Among the differentially expressed proteins associated with photosynthesis and tryptophan metabolism were up-regulated. Moreover, in gibberellin (GA) biosynthesis pathway, 10 of main enzymes of P450 were up-regulated. Proteins related to SAUR and GRP, implicated in IAA and GA signal transduction were up-regulated, and the phosphorylation and ubiquitination related proteins regulating IAA and GA signal transduction were also induced. These findings indicate that a high temperature enhances the function of photosynthesis, IAA and GA synthesis and signal transduction to promote the process of bolting, which is in line with the physiology and transcription levels of IAA and GA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivar of lettuce to restrain early bolting, which is vital for improving vegetable quality.
2019-11-12 | PXD008610 | Pride