A bacterial gene-drive system efficiently edits and inactivates a high copy number antibiotic resistance locus

J. Andrés Valderrama, Surashree S. Kulkarni, Victor Nizet () and Ethan Bier ()
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J. Andrés Valderrama: University of California, San Diego
Surashree S. Kulkarni: University of California, San Diego
Victor Nizet: University of California, San Diego
Ethan Bier: University of California, San Diego

Nature Communications, 2019, vol. 10, issue 1, 1-8

Abstract: Abstract Gene-drive systems in diploid organisms bias the inheritance of one allele over another. CRISPR-based gene-drive expresses a guide RNA (gRNA) into the genome at the site where the gRNA directs Cas9-mediated cleavage. In the presence of Cas9, the gRNA cassette and any linked cargo sequences are copied via homology-directed repair (HDR) onto the homologous chromosome. Here, we develop an analogous CRISPR-based gene-drive system for the bacterium Escherichia coli that efficiently copies a gRNA cassette and adjacent cargo flanked with sequences homologous to the targeted gRNA/Cas9 cleavage site. This “pro-active” genetic system (Pro-AG) functionally inactivates an antibiotic resistance marker on a high copy number plasmid with ~ 100-fold greater efficiency than control CRISPR-based methods, suggesting an amplifying positive feedback loop due to increasing gRNA dosage. Pro-AG can likewise effectively edit large plasmids or single-copy genomic targets or introduce functional genes, foreshadowing potential applications to biotechnology or biomedicine.

Date: 2019
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DOI: 10.1038/s41467-019-13649-6

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