ArticleBMC evolutionary biology2009
Evolutionary constraints permeate large metabolic networks.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Thermodynamics Underpinning the Microbial Community-Level Nitrogen Energy Metabolism.Environmental microbiology · 2025Article
- Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.BMC ecology and evolution · 2022Article
- Modular Evolution of the Drosophila Metabolome.Molecular biology and evolution · 2022Article
- Quantum aspects of evolution: a contribution towards evolutionary explorations of genotype networks via quantum walks.Journal of the Royal Society, Interface · 2020Article
- Metabolic Determinants of Enzyme Evolution in a Genome-Scale Bacterial Metabolic Network.Genome biology and evolution · 2018Article
- Evolution of protein-protein interaction networks in yeast.PloS one · 2017Article
- Structuring evolution: biochemical networks and metabolic diversification in birds.BMC evolutionary biology · 2016Article
- Random transposon mutagenesis of the Saccharopolyspora erythraea genome reveals additional genes influencing erythromycin biosynthesis.FEMS microbiology letters · 2015Article
- Human genome variation and the concept of genotype networks.PloS one · 2014Article
- Mathematics and evolutionary biology make bioinformatics education comprehensible.Briefings in bioinformatics · 2013Article
- Review
- Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time.Archaea (Vancouver, B.C.) · 2012Article
- Limitations of gene duplication models: evolution of modules in protein interaction networks.PloS one · 2012Article
- Expression level, cellular compartment and metabolic network position all influence the average selective constraint on mammalian enzymes.BMC evolutionary biology · 2011Article
- Structural correlations in bacterial metabolic networks.BMC evolutionary biology · 2011Article
- Dynamic network-based epistasis analysis: boolean examples.Frontiers in plant science · 2011Article
- Evolution of metabolic network organization.BMC systems biology · 2010Article
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Abstract
backgroundMetabolic networks show great evolutionary plasticity, because they can differ substantially even among closely related prokaryotes. Any one metabolic network can also effectively compensate for the blockage of individual reactions by rerouting metabolic flux through other pathways. These observations, together with the continual discovery of new microbial metabolic pathways and enzymes, raise the possibility that metabolic networks are only weakly constrained in changing their complement of enzymatic reactions.
resultsTo ask whether this is the case, I characterized pairwise and higher-order associations in the co-occurrence of genes encoding metabolic enzymes in more than 200 completely sequenced representatives of prokaryotic genera. The majority of reactions show constrained evolution. Specifically, genes encoding most reactions tend to co-occur with genes encoding other reaction(s). Constrained reaction pairs occur in small sets whose number is substantially greater than expected by chance alone. Most such sets are associated with single biochemical pathways. The respective genes are not always tightly linked, which renders horizontal co-transfer of constrained reaction sets an unlikely sole cause for these patterns of association.
conclusionEven a limited number of available genomes suffices to show that metabolic network evolution is highly constrained by reaction combinations that are favored by natural selection. With increasing numbers of completely sequenced genomes, an evolutionary constraint-based approach may enable a detailed characterization of co-evolving metabolic modules.
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