Effect of deletion of the ipdc gene, involved in indole-3-acetic acid synthesis, in the biocontrol agent Serratia plymuthica A153
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ABSTRACT:
ORGANISM(S): Serratia plymuthica
PROVIDER: GSE226107 | GEO | 2023/07/24
REPOSITORIES: GEO
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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
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
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
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
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
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
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.
2010-05-20 | GSE21737 | GEO
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
Project description:Background: The overproduction of the main auxin indole-3-acetic acid (IAA) in Sinorhizobium meliloti RD64 leads to beneficial effects both in free-living rhizobium and in host plant during symbiosis. These effects could be related to alteration in gene expression induced by IAA. Preliminary studies of these alterations induced in free-living cells have already started. In this work the transcriptional profiles of free-living S. meliloti wild type 1021 and RD64 strains obtained by RNA-seq analysis were used to better investigate this issue. Results: Transcriptome analysis by next-generation sequencing (RNA-seq) allowed the identification of the genes differentially expressed in RD64 cells, grown in a rich medium under aerobic conditions. Most of the up-regulated genes can be classified into two main categories. The first class comprised the main regulator fixJ and the two intermediate regulators fixK and nifA, which control the expression of genes involved in nitrogen-fixation. For these two latter genes the highest expression levels were observed. Several other genes, known to be FixJ targets, such as those involved in denitrification process and proline metabolism, were also identified. The second class of up-regulated genes comprised the gene coding for the sigma factor RpoH1 and other genes regulated in RpoH1-dependent manner in S. meliloti and involved in stress response. The main category of genes negatively affected can be classified in transport of sugars and other small molecules, chemotaxis and cell envelope functions. Under microaerobic condition, quantitative real-time PCR analysis of genes coding for the two-component regulatory system FixJL and for the regulator NifA showed that for all three genes the induction levels measured in RD64 cells were even higher when compared to aerobic conditions. In particular, for the fixJ gene the expression level increased more than tenfold. The up-regulation of nifA gene was also observed under aerobic conditions both when nitrogen level in the medium was limiting and when it was high. Conclusion: This work provided evidence that the overexpression of the auxin IAA in S. meliloti free-living cells triggers the induction of many genes involved in bacterial response to different abiotic stresses and allows the expression of key genes involved in nitrogen fixation. mRNA profiles of S. meliloti wild type 1021 and its derivative IAA-overproducing RD64 strain were generated in triplicate by using HiSeq2000 sequencer
2016-03-30 | E-GEOD-69880 | biostudies-arrayexpress