ArticleProceedings of the National Academy of Sciences of the United States of America2016
A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 117 papers.
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Who cites it
117 citing papers in PubMed.
- Firewalled synthetic commensal blocks horizontal gene transfer in the gut.bioRxiv : the preprint server for biology · 2026Article
- High-throughput editing boosts the construction of next-generation microbial cell factories.Synthetic and systems biotechnology · 2026Review
- Probing the limits of genetic recoding using multi-omics-guided evolution.Nature communications · 2026Article
- Gene loss and compensatory evolution as a source of metabolic preadaptations.Molecular biology and evolution · 2026Article
- Fine modulation of carbon flow in central carbon metabolism via ribosome-binding site modification inMetabolic engineering communications · 2026Article
- Optimization of the genetic code expansion technology for intracellular labelling and single-molecule tracking of proteins in genomically re-codedRSC chemical biology · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Article
- A comprehensive review of genomic-scale genetic engineering as a strategy to improve bacterial productivity.Microbiology (Reading, England) · 2025Review
- Fueling chromosomal gene diversification and artificial evolution with CRISPR.Genome biology · 2025Review
- Inducible genome-wide mutagenesis for improvement of pDNA production by E. coli.Microbial cell factories · 2025Article
- Continuous multiplexed phage genome editing using recombitrons.Nature biotechnology · 2025Article
- Rapid and Integrated Bacterial Evolution Analysis unveils gene mutations and clinical risk of Klebsiella pneumoniae.Nature communications · 2025Article
- Engineering Useful Microbial Species for Pharmaceutical Applications.Microorganisms · 2025Review
- Article
- Recent advances in targeted mutagenesis to expedite the evolution of biological systems.Journal of microbiology (Seoul, Korea) · 2025Review
- Unraveling N-Terminal Proteoform Interactomes via Multiplexed Recombineering in Salmonella.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Coselection of BAC for Escherichia coli chromosomal DNA multiplex automated genome engineering.Biotechnology letters · 2024Article
- Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools.Nature microbiology · 2024Article
- ReaL-MGE is a tool for enhanced multiplex genome engineering and application to malonyl-CoA anabolism.Nature communications · 2024Article
57 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.
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