Cargando…

Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism

Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism pro...

Descripción completa

Detalles Bibliográficos
Autores principales: Córdoba, Sandra Correa, Tong, Hao, Burgos, Asdrúbal, Zhu, Feng, Alseekh, Saleh, Fernie, Alisdair R., Nikoloski, Zoran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10425450/
https://www.ncbi.nlm.nih.gov/pubmed/37580345
http://dx.doi.org/10.1038/s41467-023-40644-9
_version_ 1785089840870588416
author Córdoba, Sandra Correa
Tong, Hao
Burgos, Asdrúbal
Zhu, Feng
Alseekh, Saleh
Fernie, Alisdair R.
Nikoloski, Zoran
author_facet Córdoba, Sandra Correa
Tong, Hao
Burgos, Asdrúbal
Zhu, Feng
Alseekh, Saleh
Fernie, Alisdair R.
Nikoloski, Zoran
author_sort Córdoba, Sandra Correa
collection PubMed
description Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism.
format Online
Article
Text
id pubmed-10425450
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-104254502023-08-16 Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism Córdoba, Sandra Correa Tong, Hao Burgos, Asdrúbal Zhu, Feng Alseekh, Saleh Fernie, Alisdair R. Nikoloski, Zoran Nat Commun Article Lipids play fundamental roles in regulating agronomically important traits. Advances in plant lipid metabolism have until recently largely been based on reductionist approaches, although modulation of its components can have system-wide effects. However, existing models of plant lipid metabolism provide lumped representations, hindering detailed study of component modulation. Here, we present the Plant Lipid Module (PLM) which provides a mechanistic description of lipid metabolism in the Arabidopsis thaliana rosette. We demonstrate that the PLM can be readily integrated in models of A. thaliana Col-0 metabolism, yielding accurate predictions (83%) of single lethal knock-outs and 75% concordance between measured transcript and predicted flux changes under extended darkness. Genome-wide associations with fluxes obtained by integrating the PLM in diel condition- and accession-specific models identify up to 65 candidate genes modulating A. thaliana lipid metabolism. Using mutant lines, we validate up to 40% of the candidates, paving the way for identification of metabolic gene function based on models capturing natural variability in metabolism. Nature Publishing Group UK 2023-08-14 /pmc/articles/PMC10425450/ /pubmed/37580345 http://dx.doi.org/10.1038/s41467-023-40644-9 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Córdoba, Sandra Correa
Tong, Hao
Burgos, Asdrúbal
Zhu, Feng
Alseekh, Saleh
Fernie, Alisdair R.
Nikoloski, Zoran
Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
title Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
title_full Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
title_fullStr Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
title_full_unstemmed Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
title_short Identification of gene function based on models capturing natural variability of Arabidopsis thaliana lipid metabolism
title_sort identification of gene function based on models capturing natural variability of arabidopsis thaliana lipid metabolism
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10425450/
https://www.ncbi.nlm.nih.gov/pubmed/37580345
http://dx.doi.org/10.1038/s41467-023-40644-9
work_keys_str_mv AT cordobasandracorrea identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism
AT tonghao identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism
AT burgosasdrubal identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism
AT zhufeng identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism
AT alseekhsaleh identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism
AT ferniealisdairr identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism
AT nikoloskizoran identificationofgenefunctionbasedonmodelscapturingnaturalvariabilityofarabidopsisthalianalipidmetabolism