Efficient site-specific recombination by self-activating split-Dre recombinase in mammalian cells and E. coli

Site-specific recombination (SSR) systems are essential tools for conditional genetic manipulation and are valued for their efficacy and user friendliness. However, the development of novel SSR strategies is urgently needed. This study aimed to identify a split Dre protein configuration that can self-activate.

By exploiting the homology between Dre and Cre, we designed a strategy to split the Dre protein at specific amino acid residues and systematically pair the resulting peptide fragments. Among these combinations, the N191/192C pair exhibited detectable recombinase activity when mediating recombination between episomal rox sites in 293T cells, whereas the other pairs presented minimal recombinase activity. Subsequent experiments revealed that the N191/192C combination efficiently mediated site-specific recombination at the integrated rox sites, without the need for auxiliary protein fusions, and demonstrated recombinase activity that is at least equivalent to that of the intact Dre protein. Interestingly, while fusion with the intein peptide increased the activity of N60/61C pair, it had a deleterious effect on the N191/192C pair. The N191/192C combination also displayed robust recombinase activity in both the murine 4T1 cell line and E. coli bacteria. Finally, our experiments demonstrated that there was no detectable cross-complementation between the split Dre and split Cre proteins.

The N191/192C split Dre protein and the intein-fused N60/61C split Dre protein can effectively mediate recombination of the integrated rox sites without the need for external signals such as light or chemical compounds. Split Dre and Cre proteins can be used together in the same cell without interfering with each other. These findings introduce new tools and strategies for gene editing and the generation of transgenic animals.