The quantitative metabolome is shaped by abiotic constraints
| Autor: | James T. Yurkovich, Amir Akbari, Bernhard O. Palsson, Daniel C. Zielinski |
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| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
Osmosis Computer science Science Physiological General Physics and Astronomy Metabolic network Computational biology Bioenergetics Biology Stress Article General Biochemistry Genetics and Molecular Biology Phosphates 03 medical and health sciences Metabolomics Stress Physiological Origin of life Metabolome Escherichia coli Phosphate Transport Proteins Magnesium Adaptation Acid stress Abiotic component Mathematical and theoretical biology Multidisciplinary Biochemical networks 030102 biochemistry & molecular biology Escherichia coli Proteins General Chemistry Phosphate Transporters Adaptation Physiological Biological Evolution Living systems 030104 developmental biology Gene Expression Regulation Acids Metabolic Networks and Pathways Hydrogen |
| Zdroj: | Nature communications, vol 12, iss 1 Nature Communications Akbari, A, Yurkovich, J T, Zielinski, D C & Palsson, B O 2021, ' The quantitative metabolome is shaped by abiotic constraints ', Nature Communications, vol. 12, 3178 . https://doi.org/10.1038/s41467-021-23214-9 Nature Communications, Vol 12, Iss 1, Pp 1-19 (2021) |
| Popis: | 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. Evolution selects for the fittest but must operate within the realm of the physically possible. Here, the authors present a theoretical framework that allows them to explore how ten abiotic constraints can shape the operation, regulation, and adaptation of metabolism in E. coli. |
| Databáze: | OpenAIRE |
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