ArticlePLoS computational biology2014
Essential plasticity and redundancy of metabolism unveiled by synthetic lethality analysis.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Uncovering coordinated pathway interactions through gene co-differential expression in yeast.Nucleic acids research · 2026Article
- Differential anaerobic oxidation of benzoate inMicrobiology spectrum · 2025Article
- Understanding flux switching in metabolic networks through an analysis of synthetic lethals.NPJ systems biology and applications · 2024Article
- Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems.Chemical reviews · 2024Review
- A parallel glycolysis provides a selective advantage through rapid growth acceleration.Nature chemical biology · 2024Article
- CRISPR-Based Therapies: Revolutionizing Drug Development and Precision Medicine.Current gene therapy · 2024Review
- Identification of risk genes for Alzheimer's disease by gene embedding.Cell genomics · 2022Article
- Computational methods, databases and tools for synthetic lethality prediction.Briefings in bioinformatics · 2022Review
- Mutation severity spectrum of rare alleles in the human genome is predictive of disease type.PLoS computational biology · 2020Article
- Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments.PLoS computational biology · 2020Article
- Evolutionary design principles in metabolism.Proceedings. Biological sciences · 2019Review
- Understanding the evolution of functional redundancy in metabolic networks.Bioinformatics (Oxford, England) · 2018Article
- A study on multi-omic oscillations in Escherichia coli metabolic networks.BMC bioinformatics · 2018Article
- Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen.Nature communications · 2018Article
- Metabolic plasticity in synthetic lethal mutants: Viability at higher cost.PLoS computational biology · 2018Article
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- Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations.Scientific reports · 2015Article
- A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors.BMC systems biology · 2014Article
- Rescue of mutant fitness defects using in vitro reconstituted designer transposons in Mycoplasma mycoides.Frontiers in microbiology · 2014Article
Corrections and comments
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Authors and funding
3 authors.
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Abstract
We unravel how functional plasticity and redundancy are essential mechanisms underlying the ability to survive of metabolic networks. We perform an exhaustive computational screening of synthetic lethal reaction pairs in Escherichia coli in a minimal medium and we find that synthetic lethal pairs divide in two different groups depending on whether the synthetic lethal interaction works as a backup or as a parallel use mechanism, the first corresponding to essential plasticity and the second to essential redundancy. In E. coli, the analysis of pathways entanglement through essential redundancy supports the view that synthetic lethality affects preferentially a single function or pathway. In contrast, essential plasticity, the dominant class, tends to be inter-pathway but strongly localized and unveils Cell Envelope Biosynthesis as an essential backup for Membrane Lipid Metabolism. When comparing E. coli and Mycoplasma pneumoniae, we find that the metabolic networks of the two organisms exhibit a large difference in the relative importance of plasticity and redundancy which is consistent with the conjecture that plasticity is a sophisticated mechanism that requires a complex organization. Finally, coessential reaction pairs are explored in different environmental conditions to uncover the interplay between the two mechanisms. We find that synthetic lethal interactions and their classification in plasticity and redundancy are basically insensitive to medium composition, and are highly conserved even when the environment is enriched with nonessential compounds or overconstrained to decrease maximum biomass formation.
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