ArticleBMC bioinformatics2004
Network analysis of metabolic enzyme evolution in Escherichia coli.
Article in BMC bioinformatics, 2004. 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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25 citing papers in PubMed, 59 citations in OpenAlex.
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- Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.BMC evolutionary biology · 2020Article
- A study on multi-omic oscillations in Escherichia coli metabolic networks.BMC bioinformatics · 2018Article
- Influence of pathway topology and functional class on the molecular evolution of human metabolic genes.PloS one · 2018Article
- Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable.Biology direct · 2016Article
- The alignment of enzymatic steps reveals similar metabolic pathways and probable recruitment events in Gammaproteobacteria.BMC genomics · 2015Article
- Biconnectivity of the cellular metabolism: A cross-species study and its implication for human diseases.Scientific reports · 2015Article
- Current understanding of the formation and adaptation of metabolic systems based on network theory.Metabolites · 2012Article
- Origins of specificity and promiscuity in metabolic networks.The Journal of biological chemistry · 2011Article
- Horizontal and vertical growth of S. cerevisiae metabolic network.BMC evolutionary biology · 2011Article
- Binding constraints on the evolution of enzymes and signalling proteins: the important role of negative pleiotropy.Proceedings. Biological sciences · 2011Review
- Evolutionary constraints permeate large metabolic networks.BMC evolutionary biology · 2009Article
- Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies.PLoS computational biology · 2008Article
- Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution.Journal of the Royal Society, Interface · 2008Review
- The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution.Genome biology · 2008Article
- Coevolution of metabolic networks and membranes: the scenario of progressive sequestration.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2007Article
- A network perspective on the topological importance of enzymes and their phylogenetic conservation.BMC bioinformatics · 2007Article
- A network perspective on the evolution of metabolism by gene duplication.Genome biology · 2007Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models. We here investigate the evolution of the metabolism in E. coli viewed as a single network using EcoCyc.
resultsSequence comparison between all enzyme pairs was performed and the minimal path length (MPL) between all enzyme pairs was determined. We find a strong over-representation of homologous enzymes at MPL 1. We show that the functionally similar and functionally undetermined enzyme pairs are responsible for most of the over-representation of homologous enzyme pairs at MPL 1.
conclusionsThe retrograde evolution model predicts that homologous enzymes pairs are at short metabolic distances from each other. In general agreement with previous studies we find that homologous enzymes occur close to each other in the network more often than expected by chance, which lends some support to the retrograde evolution model. However, we show that the homologous enzyme pairs which may have evolved through retrograde evolution, namely the pairs that are functionally dissimilar, show a weaker over-representation at MPL 1 than the functionally similar enzyme pairs. Our study indicates that, while the retrograde evolution model may have played a small part, the patchwork evolution model is the predominant process of metabolic enzyme evolution.
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