Genome-wide analysis of the auxin/indoleacetic acid (Aux/IAA) gene family in allotetraploid rapeseed (Brassica napus L.)
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ABSTRACT:
PROVIDER: PRJNA415473 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6204755_1.fastq.gz | Fastqsanger.gz | |||
| SRR6204755_2.fastq.gz | Fastqsanger.gz | |||
| SRR6204756_1.fastq.gz | Fastqsanger.gz | |||
| SRR6204756_2.fastq.gz | Fastqsanger.gz |
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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
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
Project description:Cullin RING-type E3 ubiquitin ligase SCFTIR1/AFB1-5 and their ubiquitylation targets, AUX/IAAs, sense auxin concentrations in the nucleus. TIR1 binds a surface- exposed degron in AUX/IAAs promoting their ubiquitylation and rapid auxin-regulated proteasomal degradation. Here, we resolved TIR1·auxin·IAA7 and TIR1·auxin·IAA12 complex topology, and show that flexible intrinsically disordered regions (IDRs) cooperatively position AUX/IAAs on TIR1. The AUX/IAA PB1 interaction domain also assists in non-native contacts, affecting AUX/IAA dynamic interaction states. Our results establish a role for IDRs in modulating auxin receptor assemblies. By securing AUX/IAAs on two opposite surfaces of TIR1, IDR diversity supports locally tailored positioning for targeted ubiquitylation, and might provide conformational flexibility for adopting a multiplicity of functional states. We postulate IDRs in distinct members of the AUX/IAA family to be an adaptive signature for protein interaction and initiation region for proteasome recruitment.
2020-05-27 | PXD015392 | Pride
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
Project description:BackgroundAuxin/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.ResultsIn 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.ConclusionsMembers of 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 the Aux/IAA gene family and will facilitate further dissection of Aux/IAA gene function in B. napus.
| S-EPMC5691854 | biostudies-literature
Project description:The root system plays an essential role in plant growth and adaptation to the surrounding environment. Lateral roots (LR) originate postembryonically from a group of pericycle founder cells (FC) that are specified by a root clock in an auxin dependent manner and extend the root´s surface. Auxin perception entails the physical interaction of TIR1 or AFBs proteins with Aux/IAA repressors to form a co-receptor system. Despite the apparent simplicity, how a specific TIR1/AFBs - Aux/IAA module is assembled is not completely understood. Here, we have identified and characterized a novel natural compound, called BiAux, that is a N-glucoside bisindole conjugate. This compound or rBiAux, an improved reduced form, precisely promote FC specification and lateral root emergence without affecting other auxin-related responses, including root growth. Genetic analyses demonstrated that rBiAux signaling requires the function of TIR1 and AFB2 receptors. Remarkable, rBiAux enhances TIR1 or AFB2 interaction with Aux/IAA28 and Aux/IAA18, two regulators of FCs and lateral root formation. Furthermore, rBiAux signaling seems to be dependent on ARF7, a transcription factor involved in FC specification and LR formation. Taken together, our data indicate that BiAux enhances the activity of auxin co-receptors involved in FC specification and lateral root formation.
2024-06-05 | GSE234606 | GEO
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
Project description:Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signalling network involves a negative feedback on Aux/IAA proteins which mediate the influence of auxin (the signal) on the auxin response factor (ARF) transcription factors (the drivers of the response). To probe the role of this feedback, we consider alternative in silico signalling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative feedback allows the system to have a far larger sensitivity in its dynamical response to auxin and that this sensitivity does not prevent the system from being highly resilient. Given this insight, we build a new biomolecular signalling model for quantitatively describing such Aux/IAA and ARF responses.
2022-05-10 | MODEL2003060002 | BioModels
Project description:Plants depend on the signalling of the phytohormone auxin for their development and for responding to environmental perturbations. The associated biomolecular signalling network involves a negative feedback on Aux/IAA proteins which mediate the influence of auxin (the signal) on the auxin response factor (ARF) transcription factors (the drivers of the response). To probe the role of this feedback, we consider alternative in silico signalling networks implementing different operating principles. By a comparative analysis, we find that the presence of a negative feedback allows the system to have a far larger sensitivity in its dynamical response to auxin and that this sensitivity does not prevent the system from being highly resilient. Given this insight, we build a new biomolecular signalling model for quantitatively describing such Aux/IAA and ARF responses.
2024-09-02 | BIOMD0000000927 | BioModels
Project description:In order to elucidate the molecular mechanism of auxin-induced mesocotyl elongation, gene expression profiling analyses were performed in a deep-sowing tolerant maize inbred line 3681-4. Gene expression studies combing Affymetrix GeneChip analysis and Real-time PCR were employed to determine the molecular mechanism underlying IAA promotion of maize mesocotyl elongation. Under deep-sowing condition, IAA is transported by auxin transporter-like protein 1 and binds to auxin binding protein ABP20, which results in degradation of Aux/IAA and de-repressing of auxin-inducible genes. Then, transcriptional factor such as MYB, kinase such as LRR, fructose and mannose metabolism and so on are activated. Finally, genes involved in cell wall synthesis and modification are expressed so that mesocotyl elongation of 3681-4 is promoted. Furthermore, gene expression of a key enzyme ACO in ethylene biosynthesis and ethylene receptor ETR2 were up-regulated after the treatment with 10-4 M IAA, which suggested that mesocotyl elongation of 3681-4 inclined to be inhibited when the concentration of applied IAA was increased from 10-4 M to 10-3 M. In two independent experiments, we generate 10-day-old maize mesocotyl-specific gene expression profiles through comparing genome-wide expression patterns of IAA treatment and TIBA (an auxin transportation inhibitor) treatment under 20 cm deep-sowing condition in darkness by using 17,555 Affymetrix maize whole genome array.
2009-03-26 | E-GEOD-15371 | biostudies-arrayexpress