“Programmable Removal of Bacterial Strains by Use of Genome-targeting CRISPR-Cas Systems”
Authors: Ahmed A Gomaa, Heidi E. Klumpe, Michelle L. Luo, Kurt Selle, Rodolphe Barrangou, and Chase L. Beisel, North Carolina State University
Published: online Jan. 28, in mBio
DOI: 10.1128/mBio.00928-13
Abstract: CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we demonstrate that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of “smart” antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms.
The paper, “ Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems,” is published online in the journal mBio. The paper is open access. Lead author of the paper is Ahmed Abdelshafy Gomaa, a Ph.D. student at NC State. Co-authors include Heidi Klumpe, a former undergraduate at NC State, and Michelle Luo and Kurt Selle, Ph.D. students at NC State. |
