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Novel roles, components, and mechanisms of the Escherichia coli CRISPR/Cas system

Final Report Summary - ECCRISPR (Novel roles, components, and mechanisms of the Escherichia coli CRISPR/Cas system)

We have established the CRISPR-Cas system as a weapon against antibiotic resistant bacteria. The increasing threat of pathogen resistance to antibiotics requires the development of novel antimicrobial strategies. We provided a proof of concept for a genetic strategy that aims to sensitize bacteria to antibiotics and selectively kill antibiotic-resistant bacteria. We used temperate phages to deliver a functional CRISPR-Cas system into the genome of antibiotic-resistant bacteria. The delivered CRISPR-Cas system destroyed both antibiotic resistance-conferring plasmids and genetically-modified lytic phages. This linkage between antibiotic-sensitization and protection from
lytic phages is a key feature of the strategy. It allows programming of lytic phages to kill only antibiotic-resistant bacteria while protecting antibiotic-sensitized bacteria. Phages designed according to this strategy may be used on hospital surfaces and hand-sanitizers to facilitate replacement of antibiotic-resistant pathogens with sensitive ones. We further broadened the range of bacterial targets by establishing a phage-based DNA delivery system. A major limitation in using bacteriophage-based applications is their narrow host range. Approaches for extending the host range have focused primarily on lytic phages in hosts supporting their propagation rather than approaches for extending the ability of DNA transduction into phage-restrictive hosts. To extend the host range of T7 phage for DNA transduction, we have designed hybrid particles displaying various phage tail/tail fiber proteins. These modular particles were programmed to package and transduce DNA into hosts that restrict T7 phage propagation. We have also developed an innovative generalizable platform that considerably enhances DNA transfer into new hosts by artificially selecting tails that efficiently transduce DNA. In addition, we have demonstrated that the hybrid particles can transduce desired DNA into desired hosts. This study thus critically extends and improves the ability of the particles to transduce DNA into novel phage-restrictive hosts, providing a platform for myriad applications that require this ability.
Another major achievement completed using the funding of this grant, is the elucidation of self versus foreign discrimination of DNA in the CRISPR-Cas system. In the process of CRISPR adaptation, short pieces of DNA (“spacers”) are acquired from foreign elements and integrated into the CRISPR array. It so far remained a mystery how spacers are preferentially acquired from the foreign DNA while the self chromosome is avoided. We showed that spacer acquisition is replication-dependent, and that DNA breaks formed at stalled replication forks promote spacer acquisition. Chromosomal hotspots of spacer acquisition were confined by Chi sites, which are sequence octamers highly enriched on the bacterial chromosome, suggesting that these sites limit spacer acquisition from self DNA. We further showed that the avoidance of “self” is mediated by the RecBCD dsDNA break repair complex. Our results suggest that in E. coli, acquisition of new spacers depends on RecBCD-mediated processing of dsDNA breaks occurring primarily at replication forks, and that the preference for foreign DNA is achieved through the higher density of Chi sites on the self chromosome, in combination with the higher number of forks on the foreign DNA. This model explains the strong preference to acquire spacers from both high copy plasmids and phages. These two achievements combine both basic and applicable studies of the CRISPR-Cas system, and significantly contribute to both aspects.