Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA380883 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Pathway level gating of auxin signalling provides robustness to apical stem cell fate in Arabidopsis
| PRJNA380880 | ENA
Project description:Pathway level gating of auxin signalling provides robustness to apical stem cell fate in Arabidopsis [ChIP-Seq]
| PRJNA380884 | ENA
Project description:During development and growth, dynamic signals need to be translated into spatially precise and temporally stable gene expression states, which define cell fate. In the context of the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers organ initiation. Here we show that the WUSCHEL transcription factor locally protects stem cells from differentiation by controlling the auxin signaling and response pathways via regulation of Histone acetylation. Conversely, low levels of signaling are required for stem cell maintenance, demonstrating that WUSCHEL acts as a rheostat on the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly mobile developmental signal into appropriate cell behavior with high spatial precision and temporal robustness.
2019-11-11 | GSE122610 | GEO
Project description:During development and growth, dynamic signals need to be translated into spatially precise and temporally stable gene expression states, which define cell fate. In the context of the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers organ initiation. Here we show that the WUSCHEL transcription factor locally protects stem cells from differentiation by controlling the auxin signaling and response pathways via regulation of Histone acetylation. Conversely, low levels of signaling are required for stem cell maintenance, demonstrating that WUSCHEL acts as a rheostat on the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly mobile developmental signal into appropriate cell behavior with high spatial precision and temporal robustness.
2019-11-11 | GSE122579 | GEO
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE178354 | GEO
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE156991 | GEO
Project description:In plant tissue culture, callus forms from detached explants in response to a high-auxin-to-low-cytokinin ratio on callus-inducing medium. Callus is a group of pluripotent cells because it can regenerate either roots or shoots in response to a low level of auxin on root-inducing medium or a high-cytokinin-to-low-auxin ratio on shoot-inducing medium, respectively1. However, our knowledge of the mechanism of pluripotency acquisition during callus formation is limited. On the basis of analyses at the single-cell level, we show that the tissue structure of Arabidopsis thaliana callus on callus-inducing medium is similar to that of the root primordium or root apical meristem, and the middle cell layer with quiescent centre-like transcriptional identity exhibits the ability to regenerate organs. In the middle cell layer, WUSCHEL-RELATED HOMEOBOX5 (WOX5) directly interacts with PLETHORA1 and 2 to promote TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 expression for endogenous auxin production. WOX5 also interacts with the B-type ARABIDOPSIS RESPONSE REGULATOR12 (ARR12) and represses A-type ARRs to break the negative feedback loop in cytokinin signalling. Overall, the promotion of auxin production and the enhancement of cytokinin sensitivity are both required for pluripotency acquisition in the middle cell layer of callus for organ regeneration.
2021-09-08 | GSE156990 | GEO
Project description:Identification of genes regulated by apical auxin and basal cytokinin treatment of the nodal stem in cauline buds of Arabidopsis thaliana
2016-12-25 | GSE59741 | GEO
Project description:This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol.
2011 Jul 5;7:508. 21734647
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Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex. Note:
Figure 4 of the supplementary material of the reference article has been reproduced here. In this model, the fluctuations of auxin level is represented using sinux function. Time evolution of the variables AUX/IAA (I) and mRNA (R) are plotted, under the influence of fluctuations of auxin level. pi_A is varied between 0 and 2 by steps of 0.1.
This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use
.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2011-04-01 | BIOMD0000000352 | BioModels
Project description:This is the single cell model for analysis of hormonal crosstalk in Arabidopsis described in the article:
Modelling and experimental analysis of hormonal crosstalk in Arabidopsis.
Liu J, Mehdi S, Topping J, Tarkowski P and Lindsey K. Mol Syst Biol. 2010 Jun 8;6:373; PmID: 20531403
, DOI: 10.1038/msb.2010.26
Abstract:
An important question in plant biology is how genes influence the crosstalk between hormones to regulate growth. In this study, we model POLARIS (PLS) gene function and crosstalk between auxin, ethylene and cytokinin in Arabidopsis. Experimental evidence suggests that PLS acts on or close to the ethylene receptor ETR1, and a mathematical model describing possible PLS-ethylene pathway interactions is developed, and used to make quantitative predictions about PLS-hormone interactions. Modelling correctly predicts experimental results for the effect of the pls gene mutation on endogenous cytokinin concentration. Modelling also reveals a role for PLS in auxin biosynthesis in addition to a role in auxin transport. The model reproduces available mutants, and with new experimental data provides new insights into how PLS regulates auxin concentration, by controlling the relative contribution of auxin transport and biosynthesis and by integrating auxin, ethylene and cytokinin signalling. Modelling further reveals that a bell-shaped dose-response relationship between endogenous auxin and root length is established via PLS. This combined modelling and experimental analysis provides new insights into the integration of hormonal signals in plants.
This model was originally created using Copasi and taken from the supplementary materials of the MSB article. It uses equation 5 for the auxin biosynthesis and was altered to also contain the reactions for ACC, IAA and cytokinine import. Different from the supplementary material, the parameters for the auxin synthesis, v2, are set to k2c = 0.01 uM and k2=0.2 uM_per_sec and for the WT PLS transcription k6=0.3 . To obtain the model described in the first table of the supplementary materials, set k2c=k2=0 and k6=0.9 . For the pls and PLSox mutants, k6 should be set to 0 and 0.45, respectively.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use
.
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2010-09-20 | BIOMD0000000269 | BioModels