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The quantitative metabolome is shaped by abiotic constraints
Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic constraints that define possible quantitative metabol...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155068/ https://www.ncbi.nlm.nih.gov/pubmed/34039963 http://dx.doi.org/10.1038/s41467-021-23214-9 |
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author | Akbari, Amir Yurkovich, James T. Zielinski, Daniel C. Palsson, Bernhard O. |
author_facet | Akbari, Amir Yurkovich, James T. Zielinski, Daniel C. Palsson, Bernhard O. |
author_sort | Akbari, Amir |
collection | PubMed |
description | Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic constraints that define possible quantitative metabolomes. We apply these constraints to a metabolic network of Escherichia coli that represents 90% of its metabolome. We show that the quantitative metabolomes allowed by the abiotic constraints are consistent with metabolomic and isotope-labeling data. We find that: (i) abiotic constraints drive the evolution of high-affinity phosphate transporters; (ii) Charge-, hydrogen- and magnesium-related constraints underlie transcriptional regulatory responses to osmotic stress; and (iii) hydrogen-ion and charge imbalance underlie transcriptional regulatory responses to acid stress. Thus, quantifying the constraints that the inorganic world imposes on living systems provides insights into their key characteristics, helps understand the outcomes of evolutionary adaptation, and should be considered as a fundamental part of theoretical biology and for understanding the constraints on evolution. |
format | Online Article Text |
id | pubmed-8155068 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-81550682021-06-11 The quantitative metabolome is shaped by abiotic constraints Akbari, Amir Yurkovich, James T. Zielinski, Daniel C. Palsson, Bernhard O. Nat Commun Article Living systems formed and evolved under constraints that govern their interactions with the inorganic world. These interactions are definable using basic physico-chemical principles. Here, we formulate a comprehensive set of ten governing abiotic constraints that define possible quantitative metabolomes. We apply these constraints to a metabolic network of Escherichia coli that represents 90% of its metabolome. We show that the quantitative metabolomes allowed by the abiotic constraints are consistent with metabolomic and isotope-labeling data. We find that: (i) abiotic constraints drive the evolution of high-affinity phosphate transporters; (ii) Charge-, hydrogen- and magnesium-related constraints underlie transcriptional regulatory responses to osmotic stress; and (iii) hydrogen-ion and charge imbalance underlie transcriptional regulatory responses to acid stress. Thus, quantifying the constraints that the inorganic world imposes on living systems provides insights into their key characteristics, helps understand the outcomes of evolutionary adaptation, and should be considered as a fundamental part of theoretical biology and for understanding the constraints on evolution. Nature Publishing Group UK 2021-05-26 /pmc/articles/PMC8155068/ /pubmed/34039963 http://dx.doi.org/10.1038/s41467-021-23214-9 Text en © The Author(s) 2021 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Akbari, Amir Yurkovich, James T. Zielinski, Daniel C. Palsson, Bernhard O. The quantitative metabolome is shaped by abiotic constraints |
title | The quantitative metabolome is shaped by abiotic constraints |
title_full | The quantitative metabolome is shaped by abiotic constraints |
title_fullStr | The quantitative metabolome is shaped by abiotic constraints |
title_full_unstemmed | The quantitative metabolome is shaped by abiotic constraints |
title_short | The quantitative metabolome is shaped by abiotic constraints |
title_sort | quantitative metabolome is shaped by abiotic constraints |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155068/ https://www.ncbi.nlm.nih.gov/pubmed/34039963 http://dx.doi.org/10.1038/s41467-021-23214-9 |
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