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Front Mol Biosci. 2016 Aug 31;3:45. doi: 10.3389/fmolb.2016.00045. eCollection 2016.

The Influence of Copy-Number of Targeted Extrachromosomal Genetic Elements on the Outcome of CRISPR-Cas Defense.

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Skolkovo Institute of Science and TechnologySkolkovo, Russia; Waksman Institute of Microbiology, Rutgers, The State University of New JerseyPiscataway, NJ, USA; Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia.
Department of Physics, University of Santiago de ChileSantiago, Chile; Skolkovo Institute of Science and TechnologySkolkovo, Russia.
Waksman Institute of Microbiology, Rutgers, The State University of New Jersey Piscataway, NJ, USA.


Prokaryotic type I CRISPR-Cas systems respond to the presence of mobile genetic elements such as plasmids and phages in two different ways. CRISPR interference efficiently destroys foreign DNA harboring protospacers fully matching CRISPR RNA spacers. In contrast, even a single mismatch between a spacer and a protospacer can render CRISPR interference ineffective but causes primed adaptation-efficient and specific acquisition of additional spacers from foreign DNA into the CRISPR array of the host. It has been proposed that the interference and primed adaptation pathways are mediated by structurally different complexes formed by the effector Cascade complex on matching and mismatched protospacers. Here, we present experimental evidence and present a simple mathematical model that shows that when plasmid copy number maintenance/phage genome replication is taken into account, the two apparently different outcomes of the CRISPR-Cas response can be accounted for by just one kind of effector complex on both targets. The results underscore the importance of consideration of targeted genome biology when considering consequences of CRISPR-Cas systems action.


CRISPR-Cas adaptation; CRISPR-Cas interference; bacteriophage infection; plasmid maintenance; primed adaptation

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