SLR/IAA14-dependent auxin induced lateral root initiation
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE3350 | GEO | 2005/11/01
SECONDARY ACCESSION(S): PRJNA93267
REPOSITORIES: GEO
Similar Datasets
Project description:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Experiment Overall Design: Seedlings of both wild type (Col-0) and the lateral root defective mutant (slr-1) were germinated on MS medium supplemented with 10μM NPA (=auxin transport inhibitor). Three days after germination, such seedlings were transferred to MS supplemented with 10μM NAA for 0h, 2h and 6h respectively. The segment between root meristem and root-hypocotyl junction was harvested from about 1500 seedling per time point. All treatments were repeated biologically. 5.8 μg total RNA was used for the preparation of biotinylated cRNA. Labeled RNA was hybridised to ATH1 Affymetrix chips. The resulting data was MAS5.0 normalised.
2007-07-13 | E-GEOD-3350 | biostudies-arrayexpress
Project description:To identify genes involved in the early phases of lateral root initiation, we profiled the transcriptomes of plants synchronously induced for lateral root initiation after 0, 1, 2, 4 and 6h of auxin treatment in conditions where IAA14 or IAA3-dependent auxin signaling is blocked. For this we used seedlings expressing non-degradable versions of the AUX/IAAs IAA14 (slr-1) or IAA3 (shy2-2) fused to the glucocorticoid receptor domain (slr-1:GR or shy2-2:GR) under the control of the pericycle and founder cell specific GATA23 promoter. Treatment with dexamethasone induces, specifically in pericycle cells, the nuclear translocation of the non-degradable AUX/IAA that acts as a dominant repressor of auxin signaling resulting in a complete block of lateral root formation
2018-11-20 | GSE122677 | GEO
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:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the full model described in the article.
2024-09-02 | BIOMD0000000413 | BioModels
Project description:This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73
22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.
This model corresponds to the simplified model described in the article. It is assumed that, on the timescale of DII-VENUS degradation, the concentrations of auxin, TIR1/AFB, and their complexes can be approximated by quasi-steady-state expressions. This reduced the full model to a single ODE that describes how the DII-VENUS dynamics depend on the auxin influx and four parameter groupings.
2024-09-02 | BIOMD0000000414 | BioModels
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:Auxin is a key phytohormone regulating central processes in plants that include embryo development, lateral root growth and flower maturation among others. Auxin is sensed by a set of F-Box proteins of the TIR1/AFB3 family triggering auxin dependent responses by a pathway that involves an interplay between the Aux/IAA transcription repressors and the ARF transcription factors. We have previously shown that the AFB3 auxin receptor has a specific role in coordinating primary and lateral root growth to external and internal nitrate availability (Vidal et al., 2010). In this work, we used an integrated genomics, bioinformatics and molecular genetics approach to dissect regulatory networks acting downstream AFB3 that are activated by a transient nitrate treatment in Arabidopsis roots. Our systems approach unraveled key components of the AFB3 regulatory network leading to changes in lateral root growth in response to nitrate.
2012-05-01 | GSE35544 | 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:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation. To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.
2013-08-06 | E-GEOD-35580 | biostudies-arrayexpress