Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models

Abstract Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-th...

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Autores principales:	Michael Scheunemann, Siobhan M. Brady, Zoran Nikoloski
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/4f609e4ad8c341c894b6025ccf06a70d
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spelling	oai:doaj.org-article:4f609e4ad8c341c894b6025ccf06a70d2021-12-02T15:07:51ZIntegration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models10.1038/s41598-018-26232-82045-2322https://doaj.org/article/4f609e4ad8c341c894b6025ccf06a70d2018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-26232-8https://doaj.org/toc/2045-2322Abstract Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.Michael ScheunemannSiobhan M. BradyZoran NikoloskiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-15 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Michael Scheunemann Siobhan M. Brady Zoran Nikoloski Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
description	Abstract Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.
format	article
author	Michael Scheunemann Siobhan M. Brady Zoran Nikoloski
author_facet	Michael Scheunemann Siobhan M. Brady Zoran Nikoloski
author_sort	Michael Scheunemann
title	Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
title_short	Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
title_full	Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
title_fullStr	Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
title_full_unstemmed	Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models
title_sort	integration of large-scale data for extraction of integrated arabidopsis root cell-type specific models
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/4f609e4ad8c341c894b6025ccf06a70d
work_keys_str_mv	AT michaelscheunemann integrationoflargescaledataforextractionofintegratedarabidopsisrootcelltypespecificmodels AT siobhanmbrady integrationoflargescaledataforextractionofintegratedarabidopsisrootcelltypespecificmodels AT zorannikoloski integrationoflargescaledataforextractionofintegratedarabidopsisrootcelltypespecificmodels
_version_	1718388383516983296

Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific models

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