ArticleNature communications2019
Adaptive laboratory evolution of a genome-reduced Escherichia coli.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Probing the limits of genetic recoding using multi-omics-guided evolution.Nature communications · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Exploring lipid diversity and minimalism to define membrane requirements for synthetic cells.FEBS letters · 2025Review
- Advances in adaptive laboratory evolution applications forSynthetic and systems biotechnology · 2025Review
- Engineering controllable alteration of malonyl-CoA levels to enhance polyketide production.Nature chemical biology · 2025Article
- Construction of primary chassis cells with efficient protein expression in Thermus thermophilus.Microbial cell factories · 2025Article
- The design and engineering of synthetic genomes.Nature reviews. Genetics · 2025Review
- Microbial Transcription Factor-Based Biosensors: Innovations from Design to Applications in Synthetic Biology.Biosensors · 2025Review
- Industrial Microbial Technologies for Feed Protein Production from Non-Protein Nitrogen.Microorganisms · 2025Review
- Screening of high glucose tolerant Escherichia coli for L-valine fermentation by autonomous evolutionary mutation.Applied microbiology and biotechnology · 2025Article
- Diversity of Transcriptional Regulatory Adaptation in E. coli.Molecular biology and evolution · 2024Article
- 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
- Synthetic genomes unveil the effects of synonymous recoding.bioRxiv : the preprint server for biology · 2024Article
- Article
- The functional small RNA interactome reveals targets for the vancomycin-responsive sRNA RsaOI in vancomycin-tolerantmSystems · 2024Article
- Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose.Nature communications · 2024Article
- Enhanced protein secretion in reduced genome strains of Streptomyces lividans.Microbial cell factories · 2024Article
- Strategies to identify and edit improvements in synthetic genome segments episomally.Nucleic acids research · 2023Article
- Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs.Nature communications · 2023Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain's systems biology.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.