ArticleScientific reports2020
Exploring the fitness benefits of genome reduction in Escherichia coli by a selection-driven approach.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Cas3-mediated genome reduction: demonstration in Cupriavidus necator H16 improves growth on heterotrophic and autotrophic carbon sources.Nucleic acids research · 2026Article
- Niche-specific metabolic phenotypes can be used to identify antimicrobial targets in pathogens.PLoS biology · 2024Article
- Exploiting cooperative pathogen behaviour for enhanced antibiotic potency: A Trojan horse approach.Microbiology (Reading, England) · 2024Article
- Advanced probiotics: bioengineering and their therapeutic application.Molecular biology reports · 2024Review
- Ecological dependencies and the illusion of cooperation in microbial communities.Microbiology (Reading, England) · 2024Article
- Article
- Comparative Genomics ofPHAGE (New Rochelle, N.Y.) · 2023Article
- Exploiting Cooperative Pathogen Behavior for Enhanced Antibiotic Potency: A Trojan Horse Approach.Research square · 2023Article
- Transposon sequencing identifies genes impactingInfection and immunity · 2023Article
- A self-propagating, barcoded transposon system for the dynamic rewiring of genomic networks.Molecular systems biology · 2023Article
- Engineering resource allocation in artificially minimized cells: Is genome reduction the best strategy?Microbial biotechnology · 2023Article
- Characterization of Shigella flexneri Serotype 6 Strains Isolated from Bangladesh and Identification of a New Phylogenetic Cluster.Journal of bacteriology · 2023Article
- Growth rate-associated transcriptome reorganization in response to genomic, environmental, and evolutionary interruptions.Frontiers in microbiology · 2023Article
- The rapid evolution of flagellar ion selectivity in experimental populations ofScience advances · 2022Article
- Experimental demonstration of operon formation catalyzed by insertion sequence.Nucleic acids research · 2022Article
- Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production.World journal of microbiology & biotechnology · 2022Review
- Random genome reduction coupled with polyhydroxybutyrate biosynthesis to facilitate its accumulation inFrontiers in bioengineering and biotechnology · 2022Article
- Bacterial genome reductions: Tools, applications, and challenges.Frontiers in genome editing · 2022Review
- LoxTnSeq: random transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions.Microbial biotechnology · 2021Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Artificial simplification of bacterial genomes is thought to have the potential to yield cells with reduced complexity, enhanced genetic stability, and improved cellular economy. Of these goals, economical gains, supposedly due to the elimination of superfluous genetic material, and manifested in elevated growth parameters in selected niches, have not yet been convincingly achieved. This failure might stem from limitations of the targeted genome reduction approach that assumes full knowledge of gene functions and interactions, and allows only a limited number of reduction trajectories to interrogate. To explore the potential fitness benefits of genome reduction, we generated successive random deletions in E. coli by a novel, selection-driven, iterative streamlining process. The approach allows the exploration of multiple streamlining trajectories, and growth periods inherent in the procedure ensure selection of the fittest variants of the population. By generating single- and multiple-deletion strains and reconstructing the deletions in the parental genetic background, we showed that favourable deletions can be obtained and accumulated by the procedure. The most reduced multiple-deletion strain, obtained in five deletion cycles (2.5% genome reduction), outcompeted the wild-type, and showed elevated biomass yield. The spectrum of advantageous deletions, however, affecting only a few genomic regions, appears to be limited.
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