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Implementation of stable and complex biological systems through recombinase-assisted genome engineering

Author

Listed:
  • Christine Nicole S. Santos

    (Bio Architecture Lab, Inc.
    Present address: Manus Biosynthesis, Inc., 790 Memorial Drive, Suite 102, Cambridge, Massachusetts 02139, USA)

  • Drew D. Regitsky

    (Bio Architecture Lab, Inc.
    Present address: Calysta Energy Inc., 1140 O'Brien Drive Menlo Park, California 94025, USA)

  • Yasuo Yoshikuni

    (Bio Architecture Lab, Inc.)

Abstract

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 instalment 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.

Suggested Citation

  • Christine Nicole S. Santos & Drew D. Regitsky & Yasuo Yoshikuni, 2013. "Implementation of stable and complex biological systems through recombinase-assisted genome engineering," Nature Communications, Nature, vol. 4(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3503
    DOI: 10.1038/ncomms3503
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    Cited by:

    1. Xuan Zou & Xiaohong Xiao & Ziran Mo & Yashi Ge & Xing Jiang & Ruolin Huang & Mengxue Li & Zixin Deng & Shi Chen & Lianrong Wang & Sang Yup Lee, 2022. "Systematic strategies for developing phage resistant Escherichia coli strains," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

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