ArticleNature communications2018
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Evolutionary adaptation proceeds through a small number of phenotypic modules.Molecular biology and evolution · 2026Article
- Gene loss and compensatory evolution as a source of metabolic preadaptations.Molecular biology and evolution · 2026Article
- Neisseria subflava Type 6 Secretion System competition with bacterial and fungal species.Applied microbiology and biotechnology · 2026Article
- Beyond Mendel: a call to revisit the genotype-phenotype map through new experimental paradigms.Genetics · 2026Article
- Growth dynamics of 3,909 Escherichia coli single-gene knockouts in rich and minimal media.Scientific data · 2026Article
- Macrolide resistance trajectories across threeFrontiers in microbiology · 2026Article
- Transient analysis and engineering of bacterial metabolic pathways using cell-penetrating peptide-peptide nucleic acid conjugates.Microbial cell factories · 2025Article
- Advances in adaptive laboratory evolution applications forSynthetic and systems biotechnology · 2025Review
- Construction of primary chassis cells with efficient protein expression in Thermus thermophilus.Microbial cell factories · 2025Article
- Article
- Evolution recovers the fitness of Acinetobacter baylyi strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators.PLoS genetics · 2024Article
- Experimental evolution for cell biology.Trends in cell biology · 2023Review
- A multi-scale expression and regulation knowledge base for Escherichia coli.Nucleic acids research · 2023Article
- Article
- Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network.EMBO reports · 2023Article
- An automated workflow for multi-omics screening of microbial model organisms.NPJ systems biology and applications · 2023Article
- Experimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes.mSystems · 2022Article
- Article
- Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Biological regulatory network architectures are multi-scale in their function and can adaptively acquire new functions. Gene knockout (KO) experiments provide an established experimental approach not just for studying gene function, but also for unraveling regulatory networks in which a gene and its gene product are involved. Here we study the regulatory architecture of Escherichia coli K-12 MG1655 by applying adaptive laboratory evolution (ALE) to metabolic gene KO strains. Multi-omic analysis reveal a common overall schema describing the process of adaptation whereby perturbations in metabolite concentrations lead regulatory networks to produce suboptimal states, whose function is subsequently altered and re-optimized through acquisition of mutations during ALE. These results indicate that metabolite levels, through metabolite-transcription factor interactions, have a dominant role in determining the function of a multi-scale regulatory architecture that has been molded by evolution.
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Registered trials
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