ArticlePLoS biology2021
On the optimality of the enzyme-substrate relationship in bacteria.
Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 49 citations in OpenAlex.
- Trade-off between flux efficiency and metabolic control shapes enzyme allocation.Molecular systems biology · 2026Article
- Enzyme kinetics shapes the growth response of metabolic networks.PLoS computational biology · 2026Article
- Deep Learning-Based Protein Half-Life Prediction for Identifying Rate-Limiting Enzymes in Metabolic Pathways to Alleviate Bottleneck Reactions.Journal of microbiology and biotechnology · 2026Article
- GBA Solver: a user-friendly web server for growth balance analysis.Bioinformatics (Oxford, England) · 2025Article
- Determination of α-mannan content in composite yeast cultures by enzymatic hydrolysis HPLC-UV method.Frontiers in nutrition · 2025Article
- Nonallosteric activation of posttranslational modification enzymes by active site-directed inhibitors.Computational and structural biotechnology journal · 2024Article
- Noise robustness and metabolic load determine the principles of central dogma regulation.Science advances · 2024Article
- Noise robustness and metabolic load determine the principles of central dogma regulation.ArXiv · 2024Article
- Noise robustness and metabolic load determine the principles of central dogma regulation.bioRxiv : the preprint server for biology · 2024Article
- Proteome partitioning constraints in long-term laboratory evolution.Nature communications · 2024Article
- Discretised Flux Balance Analysis for Reaction-Diffusion Simulation of Single-Cell Metabolism.Bulletin of mathematical biology · 2024Article
- Optimal enzyme profiles in unbranched metabolic pathways.Interface focus · 2024Article
- Quantifying microbial guilds.ISME communications · 2024Article
- Steering and controlling evolution - from bioengineering to fighting pathogens.Nature reviews. Genetics · 2023Review
- Decreased liver B vitamin-related enzymes as a metabolic hallmark of cancer cachexia.Nature communications · 2023Article
- Principles of metabolome conservation in animals.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Optimal density of bacterial cells.PLoS computational biology · 2023Article
- Mathematical properties of optimal fluxes in cellular reaction networks at balanced growth.PLoS computational biology · 2023Article
- Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains.eLife · 2023Article
- Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations.Nature communications · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Much recent progress has been made to understand the impact of proteome allocation on bacterial growth; much less is known about the relationship between the abundances of the enzymes and their substrates, which jointly determine metabolic fluxes. Here, we report a correlation between the concentrations of enzymes and their substrates in Escherichia coli. We suggest this relationship to be a consequence of optimal resource allocation, subject to an overall constraint on the biomass density: For a cellular reaction network composed of effectively irreversible reactions, maximal reaction flux is achieved when the dry mass allocated to each substrate is equal to the dry mass of the unsaturated (or "free") enzymes waiting to consume it. Calculations based on this optimality principle successfully predict the quantitative relationship between the observed enzyme and metabolite abundances, parameterized only by molecular masses and enzyme-substrate dissociation constants (Km). The corresponding organizing principle provides a fundamental rationale for cellular investment into different types of molecules, which may aid in the design of more efficient synthetic cellular systems.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.