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Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments

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Abstract

Recent links between computer science and synthetic biology allow for construction of many kinds of algorithmic processes within cells, obtained either by a direct engineered design or by an evolutionary search. In the latter case, horizontal gene transfer and especially transfer of plasmids by conjugation is generally respected as a crucial source of genetic diversity in bacteria. While some previous studies focused on mutations as the crucial principle to obtain diversity for engineered evolution, here we consider conjugation itself as a tool to generate diversity from a pre-determined library of biocircuits basic components. The recent development of CRISPR-Cas9 and its programmable DNA cutting ability makes it a powerful selection tool able to remove nonfunctional biocircuits from a cell population. In this paper, we describe a framework for controlled bacterial evolution of biocircuits based on conjugation and on CRISPR-Cas9, resulting in a direct biological implementation of an evolutionary algorithm. In silico experiments provide data to estimate the computational/search capability of plasmid-based engineered evolution.

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Acknowledgements

This work was supported by the European Union projects BACTOCOM (248919/FP7-ICT-2009-4), PLASWIRES (612146/FP7-ICT-FET-Proactive) and EVOPROG (610730/FP7-ICT-FET-Proactive), by the National Programme of Sustainability (NPU II) of the Czech Republic, project IT4Innovations Excellence in Science—LQ1602, by the Silesian University in Opava under the Student Funding Scheme, project SGS/13/2016, and by Spanish projects TIN2012-36992 and TIN2016-81079-R.

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Correspondence to Petr Sosík.

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Beneš, D., Rodríguez-Patón, A. & Sosík, P. Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments. Nat Comput 16, 497–505 (2017). https://doi.org/10.1007/s11047-016-9595-9

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Keywords

  • Directed evolution
  • Programmed evolution
  • Evolutionary search
  • Genetic circuit
  • Biocircuit
  • Conjugative plasmid
  • CRISPR-Cas9