Enhanced Integration of Large DNA into E. coli Chromosome By Crispr/Cas9

Mu-En Chung^1§, I-Hsin Yeh^1§, Hung Li¹, Li-Yu Sung¹, Meng-Ying Wu¹,Chun-Hung Huang¹ Yun-Peng Chao², I-Son Ng³, Yu-Chen Hu¹*

¹ Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan 300

² Department of Chemical Engineering, Feng Chia University, Taichung, Taiwan 407

³ Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan 701

Abstract

Metabolic engineering often necessitates chromosomal integration of multiple genes but integration of large genes into E. coli remains difficult. CRISPR/Cas9 is an RNA-guided system which enables site-specific induction of double strand break (DSB) and programmable genome editing. Here we hypothesized that CRISPR/Cas9-triggered DSB could enhance homologous recombination and augment integration of large DNA into E. coli chromosome. We demonstrated that CRISPR/Cas9 system was able to trigger DSB in >98% of cells, leading to subsequent cell death, and identified that mutagenic SOS response played roles in the cell survival. Acting in concert with the l-Red proteins and linear dsDNA, CRISPR/Cas9-induced DSB enabled homologous recombination of the donor DNA and replacement of lacZ gene in the MG1655 strain at efficiencies up to 99%, and allowed high fidelity, scarless integration of 2.4, 3.9, 5.4 and 7.0 kb DNA at efficiencies approaching 91%, 92%, 71% and 61%. The CRISPR/Cas9-faciliated gene integration also functioned in different E. coli strains including BL21 (DE3) and W. Our methodology facilitated precise integration of dsDNA as large as 7 kb into E. coli with efficiencies exceeding 60%, thus significantly ameliorating the editing efficiency and overcoming the size limit of integration using the commonly adopted recombineering approach.