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A role of DAO1 in oxidation of IAA amino acid conjugates revealed through metabolite, high throughput transcript and protein level analysis

ABSTRACT: After analysing auxin metabolism in auxin dependent tobacco BY-2 cell line grown in presence or absence of synthetic auxin 2,4-D we found that both conditions were similarly characterized by very low levels of endogenous indole-3-acetic acid (IAA) and its metabolites. However, metabolic profiling after exogenous application of IAA uncovered that the concentration of N-(2-oxindole-3-acetyl)-L-aspartic acid (oxIAA-Asp), the most abundantly formed auxin metabolite in the control culture, dramatically decreased in auxin-starved conditions. To describe the molecular mechanism behind this regulation, we analysed transcriptome and proteome changes caused by auxin starvation. While no changes in the expression of auxin biosynthetic machinery were observed, many genes related to auxin conjugation and degradation showed differential expression. Selected putative auxin glycosylating enzymes as well as members of the Gretchen Hagen 3 gene family involved in auxin amino acid conjugation showed both up- and down-regulation. Contrarily to that, all tobacco homologs of Arabidopsis thaliana DIOXYGENASE FOR AUXIN OXIDATION 1 (DAO1), known to be responsible for the formation of oxIAA from IAA, showed significant downregulation at both transcript and protein levels.

ORGANISM(S): Nicotiana tabacum

PROVIDER: GSE160438 | GEO | 2020/10/30

REPOSITORIES: GEO

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Variation in auxin sensing guides AUX/IAA repressor ubiquitylation and destruction

Project description:Auxin is a drug-like small molecule and morphogen that triggers the formation of SCFTIR1/AFB-AUX/IAA co-receptor complexes leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors in plants. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. TIR1-IAA19 and TIR1-IAA6 interactions form co-receptors with different affinities, which specify ubiquitylation and turnover rate of the AUX/IAA. We demonstrate lysine ubiquitylation in IAA6/IAA19 and propose this ubiquitylation signature to be a consequence of auxin-mediated SCFTIR1-AUX/IAA interactions. We present evidence for an evolving AUX/IAA repertoire, typified by the IAA6/IAA19 ohnologs, that contributes differentially to auxin sensing. We postulate that AUX/IAAs have emerged as a versatility toolbox for auxin-modulated transcriptional control, as the gamut of AUX/IAA destruction kinetics enables fine-tuning of transcriptional auxin response and contributes to the complexity of hormone signaling.

2017-06-14 | PXD004027 | Pride

Effect of long-chained auxin conjugates on gene expression in the seedlings of Brassica rapa

Project description:Auxin amino acid conjugates are considered storage forms of auxins available as a source of active auxins on the plant demand. We treated Brassica rapa seedlings with 0.01 mM indole-3-acetyl-L-alanine (IAA-Ala), indole-3-propionyl-L-alanine (IPA-Ala), and indole- 3-butyryl-L-alanine (IBA-Ala) and examined their effects on the transcriptome. All auxin conjugate treatments caused similar patterns in transcription profiles compared to the control, but with different intensities of over- and under-expression depending on the treatment. Most auxin-related DEGs were identified after IBA-Ala treatment, followed by IPA-Ala and IAA-Ala, respectively.

2024-01-17 | GSE234868 | GEO

Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)

Project description:Background: Auxin/Indoleacetic acid (Aux/IAA) genes participate in the auxin signaling pathway and play key roles in plant growth and development. Although the Aux/IAA gene family has been identified in many plants, within allotetraploid Brassica napus little is known. Results: In this study, a total of 119 Aux/IAA genes were found in the genome of B. napus. They were distributed non-randomly across all 19 chromosomes and other non-anchored random scaffolds, with a symmetric distribution in the A and C subgenomes. Evolutionary and comparative analysis revealed that 111 (94.1%) B. napus Aux/IAA genes were multiplied due to ancestral Brassica genome triplication and recent allotetraploidy from B. rapa and B. oleracea. Phylogenetic analysis indicated seven subgroups containing 29 orthologous gene sets and two Brassica-specific gene sets. Structures of genes and proteins varied across different genes but were conserved among homologous genes in B. napus. Furthermore, analysis of transcriptional profiles revealed that the expression patterns of Aux/IAA genes in B. napus were tissue dependent. Auxin-responsive elements tend to be distributed in the proximal region of promoters, and are significantly associated with early exogenous auxin up-regulation. Conclusions: The Aux/IAA gene family were identified and analyzed comprehensively in the allotetraploid B. napus genome. This analysis provides a deeper understanding of diversification of Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.

2017-10-23 | GSE105889 | GEO

Transcriptome analysis of ARF and Aux/IAA expression during the induction of somatic embryogenesis in Coffea canephora

Project description:Somatic embryogenesis (SE) is a useful biotechnological tool to study the morpho-physiological, biochemical and molecular processes during the development of Coffea canephora. Plant growth regulators (PGR) play a key role during cell differentiation in SE. The Auxin-response-factor (ARF) and Auxin/Indole-3-acetic acid (Aux/IAA) are fundamental components involved in the signaling of the IAA. The IAA signaling pathway activates or represses the expression of genes responsive to auxins during the embryogenic transition of the somatic cells. The growing development of new generation sequencing technologies (NGS), as well as bioinformatics tools, has allowed us to broaden the landscape of SE study of various plant species and identify the genes directly involved. Analysis of transcriptome expression profiles of the C. canephora genome and the identification of a particular set of differentially expressed genes (DEG) during SE are described in this study. A total of eight ARF and seven Aux/IAA differentially expressed genes were identified during the different stages of the SE induction process. The quantitative expression analysis showed that ARF18 and ARF5 genes are highly expressed after 21 days of the SE induction, while Aux/IAA7 and Aux/IAA12 genes are repressed. The results of this study allow to have a better understanding of the genes involved in auxin signaling pathway as well as their expression profiles during the SE process.

2019-04-03 | GSE128888 | GEO

The small signalling peptide CEP5 attenuates the dynamic AUX/IAA equilibrium

Project description:Root architecture is vital for plant growth and largely depends on primary root growth and lateral root development. Several plant hormones have been shown to affect root architecture among which auxin has been granted a central role. Lately, small signalling peptides also emerged as potential molecular components regulating root growth and development. Here, we identified C-TERMINALLY ENCODED PEPTIDE 5 (CEP5) as a novel, phloem poleexpressed paracrine signal for lateral root initiation. Our genetic, biochemical and pharmacological results show that CEP5 counteracts auxin signalling by stabilizing AUXIN/INDOLE ACETIC ACID (AUX/IAA) transcriptional repressors, suggesting the existence of an additional control mechanism through which plants can attenuate auxin signalling in a developmental context. Reducing CEP5 expression levels resulted in an increased auxin response and subsequently interfered with the normal progression through lateral root developmental stages.

2022-03-01 | PXD002589 | Pride

Transcriptomic analysis of IAA treated 3 DAG WT and er erl2 seedlings.

Project description:Proper control of Auxin localization and accumulation are essential for leaf primordia initiation. Additionally, previous work has shown that the ERECTA family of genes also control leaf initiation. In this study we seek to understand the interaction between Auxin and the er erl2 double mutant in 3 days after germination (DAG) old seedlings. WT and mutant seedlings were either treated with IAA or mock treatments for 30 minutes. RNA was isolated and poly-A enriched strand specific libraries were constructed and paired end sequencing was carried out. The mutant showed mild, yet consistent enrichment of chloroplast and carbohydrate metabolism gene ontology terms in our mutant compared to WT. However, at 30 minutes post IAA treatment, the mutant and WT did not have significantly different responses to auxin. This indicates that the ERECTA family genes do not play a significant role in the immediate and direct response to auxin.

2022-02-25 | GSE197154 | GEO

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

Comparative transcriptome analysis reveals the promoting effects of IAA on biomass production and branching of Gracilariopsis lemaneiformis

Project description:Purpose: Gracilariopsis lemaneiformis is one of main economical species cultivated seaweed in China. The yield of G. lemaneiformis was positive related with its rhizoid branching number and length, whereas the regulation on branching and growth of G. lemaneiformis was unclear. IAA was well known to control morphogenesis and growth in land plants. This study aimed to evaluate the roles of IAA on the growth and branch formation of G. lemaneiformis rhizoids. Methods: Total RNA was extracted from G. lemaneiformis with branch and 2 cm of primary branch at 1 and 3 d after IAA treatment, respectively using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Three biological replicates are included for a treatment. RNA-seq were conducted by BGI, Shenzhen. Trinity (v2.0.6) was used to assemble the clean reads and Tgicl (v2.0.6) to perform clustering and eliminate redundant data in the assembled transcripts to obtain unique genes. Results: IAA could activate the pathways in ABCB auxin transporters, precursor biosynthesis of growth-related hormones and plant hormone signal transduction. IAA promoted the precursors synthesis of CTKs, GAs and BR and activated the ARFs involved in IAA signal transduction, and ARR-A and ARR-B involved in CTKs signal transduction, which further regulate the genes encoding cyclin-dependent kinases, cyclins, tubulin, and cell division cycle involved in cell division process. Meanwhile, carbon fixation, carbohydrate metabolism, energy metabolism, and amino acid biosynthesis and metabolism were also responsive to IAA, revealed that IAA induced to produce more energy and metabolic intermediates for cell growth.

2021-12-31 | GSE185906 | GEO

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

2010-05-20 | GSE21737 | GEO

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