Auxin-mediated gene expression in WT, iaa17, axr3 and iaa5iaa6iaa19 mutants
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE629 | GEO | 2005/12/01
SECONDARY ACCESSION(S): PRJNA87535
REPOSITORIES: GEO
Similar Datasets
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:RNA samples were extracted from liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Lines used for this study: Columbia wild-type nph4-1(arf7) single mutant arf19-1 single mutant nph4-1 arf19-1 double mutant Treatment: Control (EtOH) Auxin treated (5µM IAA) Keywords = Auxin Keywords = Auxin response factor Keywords: parallel sample
2005-10-19 | GSE627 | GEO
Project description:RNA samples were extracted from liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Lines used for this study: Columbia wild-type nph4-1(arf7) single mutant arf19-1 single mutant nph4-1 arf19-1 double mutant Treatment: Control (EtOH) Auxin treated (5µM IAA) Keywords = Auxin Keywords = Auxin response factor Keywords: parallel sample
2010-06-09 | E-GEOD-627 | biostudies-arrayexpress
Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations. Data analysis: Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The “R” environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis. Keywords = Auxin Keywords = Auxin response factor Keywords: other
2005-10-19 | GSE631 | GEO
Project description:Global gene expression data from 7-day old light-grown liquid cultured seedlings treated with or without auxin (5µM IAA) for 2 h. Columbia (WT) and Auxin response factor 2 (ARF2) T-DNA insertion mutant (arf2-6 ) were used for this study. Each experimental condition has three true replicates for a total of 12 hybridizations. Data analysis:; Affymetrix GeneChip Microarray Suite version 5.0 software was used to obtain signal values for individual genes. The data files containing the probe level intensities (cell files) were used for background correction and normalization using the log2 scale robust multi-array analysis (RMA) procedure (Irizarry et al., 2003). The âRâ environment (Ihaka and Gentleman, 1996) was used for running the RMA program. Data analysis and statistical extraction were performed using log2 converted expression intensity data within Microsoft Excel 98. Based on preliminary analysis, a hybridization signal less than 5.64385619 (= log2 50) was considered as background; all signals less than 5.64385619 were converted to 5.64385619 prior to further analysis.
2008-06-14 | E-GEOD-631 | biostudies-arrayexpress
Project description:Recently, 2-aminoxy-3-phenylpropionic acid (L-AOPP) had been demonstrated to possess an inhibitory activity against IAA biosynthesis but the molecular basis of the action was unclear. To investigate the function of L-AOPP, we conducted microarray analysis using the shoot apical meristem (SAM) part of A. thaliana in addition to whole plants after the treatment of L-AOPP. We performed microarray analysis using the shoot apical meristem (SAM) part of A. thaliana (Columbia-0) to investigate function of 2-aminoxy-3-phenylpropionic acid (L-AOPP) in relation to inhibition of auxin biosynthesis. Total RNA was extracted from SAM part of 7-day-old seedlings grown on 1/2 MS medium containing L-AOPP (50 µM),L-AOPP (50 µM) + Indole-3-acetic acid (IAA 10 nM) or Dimethyl sulfoxide (DMSO 0.1%).
2015-12-31 | E-GEOD-30092 | biostudies-arrayexpress
Project description:Azospirillum is a plant growth promoting rhizobacteria (PGPR) with ability to produce several phytohormones such as auxins, mainly indole-3-acetic acid (IAA). The positive interaction of Azospirillum with plants has been simplified and explained through the bacterial capacity to produce IAA. Typical changes on root architecture by promoting the number of lateral roots and hair formation, and reducing the primary root length were established in inoculated plants. These changes increase the root surface improving the water and nutrients acquisition, and thus the growth of the whole plant. The mechanisms by which Azospirillum induces such changes fails to be explained only by the bacterial capacity to produce IAA. In this work, we have evaluated the root architecture and gene expression changes occurred in Arabidopsis thaliana inoculated with A. brasilense Az39 and the IAA-deficient mutant (Az39 ipdC-), or treated with exogenous IAA solution to confirm both, the IAA-dependent and IAA-independent Azospirillum´s pathways to promote the root growth. Our results demonstrate the ability of Az39 to modify the primary root development through IAA biosynthesis, while other IAA-independent mechanisms were related to an increase in the lateral roots development and the root hairs number. Jasmonates, ethylene and salicylic acid were increased in the IAA-deficient bacterial treatments, as the ipdC mutant significantly up-regulated transcription of genes enriched of these phytohormones signaling after 7 days. Further, the physical presence of the inactive bacteria (Az39φ) seems to mediate the development of root hairs, a mechanism common to other non-PGPR as E. coli DH5α. Our results suggest that Az39 inoculation induces morphological changes in root architecture through both IAA-dependent and independent mechanism. The IAA biosynthesis by Az39 reduces the primary root length; while the cells contact with the roots increases the root hairs production. Both the synthesis of active IAA and the presence of metabolically active Az39 cells increase the growth and development of lateral roots.
2021-12-24 | GSE192383 | GEO
Project description:Wild tobacco flowers wave rhythmically to facilitate specific pollinator interactions. This movement behavior is controlled by a regulatory network that involves the circadian clock- and auxin-signaling pathways. The plant hormone auxin, similarly to its function in tropic movements, acts as growth regulator in the circadian regulation of floral movement. Dorsoventral asymmetry in auxin levels and auxin transcriptional responses mediate the growth responses in the floral peduncle that make flowers move. Multiple components of the auxin-signaling pathway and auxin responses are under the control of circadian clock. However, it is unclear where these two pathways intersect and how collectively contribute to regulate specific rhythmic outputs. Here we found that the blue light photoreceptor and circadian clock component ZEITLUPE (ZTL) controls auxin responses through the regulation of the auxin-signaling pathway in a time-of-day and blue light specific manner. Abrogation of ZTL expression abolishes flower movement and the temporal gating of auxin-induced growth responses in the floral peduncle. ZTL regulates transcription and directly interacts with indole-3-acetic acid inducible 19 (IAA19), a circadian controlled gene that regulates development of curvature in moving organs. Indicating that ZTL modulates auxin sensitivity in part through the regulation of AUX/IAA transcriptional repressors. At night, growth responses in the peduncle to the synthetic auxin 2,4-D revealed that ZTL additionally controls auxin responses regulating auxin homeostasis. These results indicate that ZTL conveys temporal and environmental information, at multiple levels, into the auxin signaling-pathway and in this way sculpts the temporal gating of auxin responses that allow flowers to move. To gain further insight into the molecular basis of temporal regulation of the movement of flowers we used a whole genome microarray as a discovery platform to identify genes differentially expressed in a RNAi knockdown line silenced in the expression of the circadian clock component ZEITLUPE (irZTL-314).
2019-06-30 | GSE116648 | GEO
Project description:Although a wide range of interactions between BRs and auxin have been recognized, knowledge about the direct molecular mechanism of interaction between them in specific physiological processes is very limited. In this study we found that auxin resisitent mutant msg2/iaa19 and arf7 were also resisitant to the BR effect on morphogenensis of dark-grown Arabidosis seedlings. Moreover, BR signaling transcription factor BZR1 can directly bind to promoter regions of IAA19 and ARF7. Microarray analysis revealed that a number of gene transcripts showed reduced BR response in msg2 and the control mutant axr2, suggesting the crucial role of IAA19 in mediating BR effects. Taken together, our results suggested that BRs regulate morphogenesis of dark-grown seedling by employing auxin signaling components IAA19 and ARF7.
2012-12-16 | GSE33412 | GEO
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. Keywords: time-course wild type vs mutant comparison
2005-11-01 | GSE3350 | GEO