ArticleNature communications2021
The quantitative metabolome is shaped by abiotic constraints.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models.Nature protocols · 2026Article
- Review
- Article
- Multi-scale reactor designs extend the physical limits ofbioRxiv : the preprint server for biology · 2024Article
- Article
- Metabolic homeostasis and growth in abiotic cells.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Prediction of metabolite-protein interactions based on integration of machine learning and constraint-based modeling.Bioinformatics advances · 2023Article
- Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism.PLoS computational biology · 2022Article
- The hidden simplicity of metabolic networks is revealed by multireaction dependencies.Science advances · 2022Article
- Article
- Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium.PLoS computational biology · 2021Article
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Authors and funding
4 authors.
Funding
Abstract
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.
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