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

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.