Implementation of stable and complex biological systems through recombinase-assisted genome engineering
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Evaluating the performance of engineered biological systems with high accuracy and precision is nearly impossible with the use of plasmids due to phenotypic noise generated by genetic instability and natural population dynamics. Minimizing this uncertainty therefore requires a paradigm shift towards engineering at the genomic level. Here, we introduce an advanced design principle for the stable installment and implementation of complex biological systems through recombinase-assisted genome engineering (RAGE). We apply this concept to the development of a robust strain of Escherichia coli capable of producing ethanol directly from brown macroalgae. RAGE significantly expedites the optimal implementation of a 34 kb heterologous pathway for alginate metabolism based on genetic background, integration locus, copy number and compatibility with two other pathway modules (alginate degradation and ethanol production). The resulting strain achieves a ~40% higher titre than its plasmid-based counterpart and enables substantial improvements in titre (~330%) and productivity (~1,200%) after 50 generations.
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The resulting engineered strain, which integrates alginate metabolism genes into its genome, produced a 330% higher titer than the canonical plasmid-based E. coli counterpart after culturing both strains on synthetic seaweed medium for 50 generations.
“The resulting engineered strain, which integrates alginate metabolism genes into its genome, produced a 330% higher titer than the canonical plasmid-based E. coli counterpart after culturing both strains on synthetic seaweed medium for 50 generations (Santos et al., 2013).”
From The Enzymatic Conversion of Major Algal and Cyanobacterial Carbohydrates to Bioethanol (2016) · cites this paper as Santos et al., 2013
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De novo design of biosynthetic pathways for bacterial production of bulk chemicals and biofuels
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Biological conversion of cyclic ketones from catalytic fast pyrolysis with Pseudomonas putida KT2440
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On the Choice of the Right Plasmid Vector(s) in the Times of Synthetic Biology
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- Authors
- Santos, C. N. S., Regitsky, D. D., & Yoshikuni, Y.
- Corresponding author
- Yoshikuni, Yasuo
- Venue
- Nature Communications
- Published
- 2013-09-23
- Volume
- 4
- Issue
- 1
- Pages
- 2503-2503
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W2080365353
- Cited by
- 93
- References
- 42
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 8 · 2023: 6 · 2022: 12 · 2021: 9 · 2020: 9 · 2019: 8 · 2018: 3 · 2017: 3 · 2016: 16 · 2015: 4 · 2014: 4 · 2013: 1
- FWCI
- 3.73
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Nature Communications (publishedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- U.S. Department of Energy
- Corporación de Fomento de la Producción
- Advanced Research Projects Agency - Energy (DE-AR0000006)
- Advanced Research Projects Agency
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Escherichia coli, brown macroalgae, ethanol production, chromosomal integration, plasmid instability, phenotypic noise, genetic background, copy number, strain robustness
- MeSH terms
- Ethanol, Phaeophyceae, Alginates, Escherichia coli, Genetic Engineering, Hexuronic Acids, Plasmids, Mutagenesis, Insertional, Genome, Bacterial, Glucuronic Acid, Escherichia coli Proteins, Recombinases, Metabolic Networks and Pathways
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