Root nitrate response of Ws plants and afb3-1 mutant plants
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE35544 | GEO | 2012/05/01
SECONDARY ACCESSION(S): PRJNA152275
REPOSITORIES: GEO
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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. Arabidopsis seedlings of the Ws and afb3-1 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 μE/m2/sec) and 8 hours of dark at 22°C for 14 days. The plants were treated at the onset of the light cycle with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Whole roots were cut from seedlings and frozen on liquid Nitrogen. Total RNA was extracted using the TriZol reagent. 3 independent biological replicates were performed.
2012-04-30 | E-GEOD-35544 | biostudies-arrayexpress
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:In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative downstream components of the nitrate regulation of lateral root development was investigated. To this aim, the endogenous SL content of maize root in response to nitrate availability was assessed by means of LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, un untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolacotones to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation toughly induces zealactone and carlactonoic acid biosynthesis in maize root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise the existence of both auxin-dependent and auxin-independent effects of nitrate on LR development. In addition, the inhibition of SL biosynthesis seems to participate to the auxin-dependent induction of LR, but the involvement of further downstream unknown components cannot be ruled out.
2021-04-11 | GSE162411 | GEO
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:Nitrate regulates plant growth and development and acts as a potent signal to control gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis thaliana roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly and quickly after nitrate treatments in root organs in a tissue-specific manner. Phenotypic analysis of tga1/tga4 double mutant plants indicated that TGA1 and TGA4 are necessary for nitrate modulation of both primary and lateral root growth. Global gene expression analysis revealed that 97% of the genes with altered expression in tga1/tga4 double mutant plants are regulated by nitrate treatments indicating these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. Among the nitrate-responsive genes that depend on TGA1/TGA4 for normal regulation of gene expression, we found nitrate transporters NRT2.1, NRT2.2 and nitrite reductase (NIR) genes. Specific binding of TGA1 to its cognate DNA sequence on the target gene promoters was confirmed by chromatin immunoprecipitation assays. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots.
2013-03-31 | GSE43011 | 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: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: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: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:Nitrate regulates plant growth and development and acts as a potent signal to control gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis thaliana roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly and quickly after nitrate treatments in root organs in a tissue-specific manner. Phenotypic analysis of tga1/tga4 double mutant plants indicated that TGA1 and TGA4 are necessary for nitrate modulation of both primary and lateral root growth. Global gene expression analysis revealed that 97% of the genes with altered expression in tga1/tga4 double mutant plants are regulated by nitrate treatments indicating these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. Among the nitrate-responsive genes that depend on TGA1/TGA4 for normal regulation of gene expression, we found nitrate transporters NRT2.1, NRT2.2 and nitrite reductase (NIR) genes. Specific binding of TGA1 to its cognate DNA sequence on the target gene promoters was confirmed by chromatin immunoprecipitation assays. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots. Arabidopsis seedlings of the Col-0 and tga1/tga4 genotypes were grown on hydroponic medium containing 1X MS salts without Nitrogen, supplemented with 0.5 mM ammonium succinate as Nitrogen source and 3 mM sucrose on a Percival chamber under a photoperiod of 16 hours of light (100 ?E/m2/sec) and 8 hours of dark at 22°C for 14 days. The plants were treated at the onset of the light cycle with 5 mM KNO3 or 5 mM KCl as control for 2 hours. Whole roots were cut from seedlings and frozen on liquid Nitrogen. Total RNA was extracted using the TriZol reagent. 3 independent biological replicates were performed.
2013-03-31 | E-GEOD-43011 | biostudies-arrayexpress