ArticleMolecular systems biology2011
Metabolic modeling of endosymbiont genome reduction on a temporal scale.
Article in Molecular systems biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Quantitative principles of microbial metabolism shared across scales.Nature microbiology · 2024Review
- Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments.Communications biology · 2024Article
- PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways.BMC bioinformatics · 2024Article
- Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.BMC ecology and evolution · 2022Article
- Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genusMicrobial genomics · 2020Article
- Less Is More: Genome Reduction and the Emergence of Cooperation-Implications into the Coevolution of Microbial Communities.International journal of genomics · 2019Review
- Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss.BMC systems biology · 2018Article
- Testing the Domino Theory of Gene Loss inLife (Basel, Switzerland) · 2018Article
- Ecology and Evolution of Chromosomal Gene Transfer between Environmental Microorganisms and Pathogens.Microbiology spectrum · 2018Article
- Modeling cancer metabolism on a genome scale.Molecular systems biology · 2015Review
- Article
- Systems biology perspectives on minimal and simpler cells.Microbiology and molecular biology reviews : MMBR · 2014Review
- Genome reduction as the dominant mode of evolution.BioEssays : news and reviews in molecular, cellular and developmental biology · 2013Article
- Inferring ancient metabolism using ancestral core metabolic models of enterobacteria.BMC systems biology · 2013Article
- Short and long-term genome stability analysis of prokaryotic genomes.BMC genomics · 2013Article
- Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.Molecular systems biology · 2013Review
- Studying the relationship between robustness against mutations in metabolic networks and lifestyle of organisms.TheScientificWorldJournal · 2013Article
- F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks.BMC bioinformatics · 2012Article
- Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.Nature reviews. Microbiology · 2012Review
- Metabolic stasis in an ancient symbiosis: genome-scale metabolic networks from two Blattabacterium cuenoti strains, primary endosymbionts of cockroaches.BMC microbiology · 2012Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A fundamental challenge in Systems Biology is whether a cell-scale metabolic model can predict patterns of genome evolution by realistically accounting for associated biochemical constraints. Here, we study the order in which genes are lost in an in silico evolutionary process, leading from the metabolic network of Escherichia coli to that of the endosymbiont Buchnera aphidicola. We examine how this order correlates with the order by which the genes were actually lost, as estimated from a phylogenetic reconstruction. By optimizing this correlation across the space of potential growth and biomass conditions, we compute an upper bound estimate on the model's prediction accuracy (R=0.54). The model's network-based predictive ability outperforms predictions obtained using genomic features of individual genes, reflecting the effect of selection imposed by metabolic stoichiometric constraints. Thus, while the timing of gene loss might be expected to be a completely stochastic evolutionary process, remarkably, we find that metabolic considerations, on their own, make a marked 40% contribution to determining when such losses occur.
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