Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of deletion of the ipdc gene, involved in indole-3-acetic acid synthesis, in the biocontrol agent Serratia plymuthica A153

ABSTRACT: To explore the role of indole-3-acetic acid (IAA) as signalling molecule in plant-associated bacteria we analyzed the whole transcriptome of S. plymuthica A153 wild type and its Δipdc mutant in vitro

ORGANISM(S): Serratia plymuthica

PROVIDER: GSE226107 | GEO | 2023/07/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Indole-3-acetic acid degradation in a novel strain Pseudomonas composti LY1

Project description:Indole-3-acetic acid (IAA), knows as common plant hormone, is one of the most distributed indole derivatives in the environment. A novel strain, which was able to use IAA as sole source of carbon and nitrogen, was isolated from farm soil, identified and classified as Pseudomonas composti LY1 based on 16S rRNA sequence and genome analysis. The optimal growth conditions for LY1 with IAA are characterized. Proteome profile of strain LY1 to IAA and citrate were analyzed and compared using label free strategy with LC-MS/MS.

2021-09-08 | PXD014968 | Pride

iac gene expression in the indole-3-acetic acid-degrading soil bacterium Enterobacter soli LF7

Project description:We show for soil bacterium Enterobacter soli LF7 (synonym Enterobacter asburiae LF7a) that possession of a iac (indole 3-acetic acid catabolic) gene cluster is causatively linked to the ability to utilize the plant hormone indole 3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. Also highly induced and immediately downstream of the iac cluster were genes for a Major Facilitator Superfamily protein (mfs) and enzymes of the β-ketoadipate pathway (pcaIJD-catBCA), which channels catechol into central metabolism. This entire iacHABICDEFG-mfs-pcaIJD-catBCA gene set was constitutively expressed in a iacR deletion mutant, confirming the role of iacR, annotated as coding for a MarR-type regulator and located upstream of iacH, as a repressor of iac gene expression. The research described here was funded from grants #2010-03544 and #2013-02075 awarded to JHJL by the United States Department of Agriculture (USDA) National Institute of Food and Agriculture (NIFA) Agriculture and Food Research Initiative (AFRI)

2018-05-05 | GSE114050 | GEO

Gut Microbiota Metabolite Indole-3-Acetic Acid Maintains Intestinal Epithelial Homeostasis Through Mucin Sulfation

Project description:The incidence and prevalence of inflammatory bowel disease (IBD) is gradually increasing. A high-fat diet (HFD) is known to disrupt intestinal homeostasis and aggravate IBD, yet the underlying mechanisms remain largely undefined. Here, a positive correlation between dietary fat intake and disease severity in both IBD patients and HFD-fed mice is observed. HFD induces a significant decrease in indole-3-acetic acid (IAA) and lead to intestinal barrier damage. Furthermore, IAA supplementation enhances the intestinal mucin sulfation and effectively alleviates colitis. Mechanistically, IAA upregulates key molecules involved in mucin sulfation, including Papss2 and Slc35b3, the synthesis enzyme and the transferase of 3'-phosphoadenosine-5'-phosphosulfate (PAPS), via the Aryl Hydrocarbon Receptor (AHR). More importantly, AHR can directly bind to the transcription start site of Papss2. Oral administration of Lactobacillus reuteri, which can produce IAA, contributes to protecting against colitis and promoting mucin sulfation, while the modified L. reuteri strain lacking the iaaM gene (LactobacillusΔiaaM) and the ability to produce IAA fails to exhibit such effects. Overall, IAA enhances intestinal mucin sulfation through AHR, contributing to the protection of intestinal homeostasis.

2024-05-26 | GSE249996 | GEO

Effect of deletion of the ipdc gene, involved in indole-3-acetic acid synthesis, in the biocontrol agent Serratia plymuthica A153

Project description:Effect of deletion of the ipdc gene, involved in indole-3-acetic acid synthesis, in the biocontrol agent Serratia plymuthica A153

| PRJNA938515 | ENA

Characterization of indole-3-acetic acid biosynthesis and the effects of IAA exposure on the proteome of the plant-associated microbe Pantoea sp. YR343

Project description:Pantoea sp. YR343, isolated from the Populus deltoides rhizosphere, is a robust plant root colonizer that produces indole-3-acetic acid (IAA). Genomic and metabolomic analyses predicted that Pantoea sp. YR343 synthesizes IAA primarily using the indole-3-pyruvate pathway. Pantoea sp. YR343 proteomes showed upregulation of IpdC for growth in the presence of tryptophan or IAA versus controls.

2017-08-23 | MSV000081478 | MassIVE

Expression data from Arabidopsis wild type and ibr1 ibr3 ibr10 triple mutant seedlings root tip segments treated with indole-3-butyric acid (IBA)

Project description:The root cap-specific conversion of the auxin precursor indole-3-butyric acid (IBA) into the main auxin indole-3-acetic acid (IAA) generates a local auxin source which subsequently modulates both the periodicity and intensity of auxin response oscillations in the root tip of Arabidopsis, and consequently fine-tunes the spatiotemporal patterning of lateral roots. To explore downstream components of this signaling process, we investigated the early transcriptional regulations happening in the root tip during IBA-to-IAA conversion in Col-0 and ibr1 ibr3 ibr10 triple mutant after 6 hours of IBA treatment.

2015-05-12 | GSE59426 | GEO

Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole-3-acetic acid (IAA)

Project description:Nitrogen (N) and phosphorus (P) are the most limiting factors for plant growth. Some microorganisms improve the uptake and availability of N and P, minimizing chemical fertilizer dependence. It has been published that the RD64 strain, a Sinorhizobium meliloti 1021 strain engineered to overproduce indole-3-acetic acid (IAA), showed improved nitrogen fixation ability as compared to the wild type 1021 strain. We present here data showing that RD64 is also highly effective in mobilizing P from insoluble sources such as phosphate rock (PR). Under P-limiting conditions, the higher P-mobilizing activity of RD64, as compared to the 1021 wild type strain, is connected with the up-regulation of genes coding for the high-affinity P transport system, the induction of acid phosphatase activity and the increased secretion into the growth media of malic, succinic and fumaric acids. Medicago truncatula plants nodulated by RD64 (Mt-RD64), when grown under P-deficient conditions, released higher amounts of another P-solubilizing organic acid, the 2-hydroxyglutaric acid, as compared to the plants nodulated by the wild-type strain (Mt-1021). It has already been shown that Mt-RD64 plants exhibited a higher dry weight production as compared to Mt-1021 plants. Here we report that also P-starved Mt-RD64 plants show a significant increase both in shoot and root fresh weight when compared to P-starved Mt-1021 plants. We discuss how, in a rhizobium-legume model system, a balanced interplay of different factors linked to the bacterial IAA over-production rather than IAA production per se stimulates plant growth under stressful environmental conditions, and in particular, under P-starvation. Two-conditions experiment: untreated 1021 vs. IAA-treated 1021 cells. Biological replicates: 6 untreated controls, 6 treated samples, independently grown and harvested. One replicate per array.

2010-05-20 | E-GEOD-21737 | biostudies-arrayexpress

Transcription profiling of indole-3-acetic acid at physiological concentrations (IAA) treatment of Arabidopsis seedlings

Project description:To demonstrate the analysis of differential expression using CATMA v1 arrays, Arabidopsis seedlings were treated with indole-3-acetic acid at physiological concentrations. The seedlings were germinated in liquid medium, and treated with indole-3-acetic acid for 30, 120 or 240 minutes. Changes in expression patterns were monitored using a complete loop design including an untreated sample (0 minutes). Reciprocal labelling was used rendering a total of eight hybridisations. An additional self-to-self hybridisation for time-point 0 was included. The statistical analysis was based an ANOVA model and indicated that 1123 GSTs were differentially expressed (p < 2.37 x 10-6) in at least one of the three time points following treatment.

2004-05-31 | E-MEXP-65 | biostudies-arrayexpress

Sinorhizobium meliloti cells: untreated 1021 strain vs. 1021 treated with indole-3-acetic acid (IAA)

2010-05-20 | GSE21737 | GEO

Bj_indole-3-acetic acid 1 mM vs. non-treatment

Project description:Transcriptional profiling of mid-logarithmic phase cultures exposed to a 1 mM shock treatment of indole-3-acetic acid for 3 hours.

2013-06-01 | GSE36913 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data