ArticlePLoS computational biology2018
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 20 citations in OpenAlex.
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- Genome-scale metabolic modelling of extremophiles and its applications in astrobiological environments.Environmental microbiology reports · 2024Review
- Functional comparison of metabolic networks across species.Nature communications · 2023Article
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- Genome-scale metabolic modeling in antimicrobial pharmacology.Engineering microbiology · 2022Review
- Search for a Shared Genetic or Biochemical Basis for Biofilm Tolerance to Antibiotics across Bacterial Species.Antimicrobial agents and chemotherapy · 2022Article
- A synthetic 'essentialome' for axenic culturing of 'Candidatus Liberibacter asiaticus'.BMC research notes · 2022Article
- TheMicrobiology spectrum · 2021Article
- The metabolic network of the last bacterial common ancestor.Communications biology · 2021Article
- Novel antimicrobial development using genome-scale metabolic model of Gram-negative pathogens: a review.The Journal of antibiotics · 2021Review
- The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes.Nucleic acids research · 2021Article
- Flux-based hierarchical organization of Escherichia coli's metabolic network.PLoS computational biology · 2020Article
- ePath: an online database towards comprehensive essential gene annotation for prokaryotes.Scientific reports · 2019Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene essentiality datasets encompassing a wide variety of species of bacteria and archaea. Conservation of metabolic genes was estimated by analysing 79 representative genomes from all the branches of the prokaryotic tree of life. We find that essentiality patterns reflect phylogenetic relations both for modelling and experimental data, which correlate highly at the pathway level. Genes that are essential for several species tend to be highly conserved as opposed to non-essential genes which may be conserved or not. The tRNA-charging module is highlighted as ancestral and with high centrality in the networks, followed closely by cofactor metabolism, pointing to an early information processing system supplied by organic cofactors. The results, which point to model improvements and also indicate faults in the experimental data, should be relevant to the study of centrality in metabolic networks and ancient metabolism but also to metabolic engineering with prokaryotes.
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