Unique properties of spacer acquisition by the type III-A CRISPR-Cas system

Type III CRISPR-Cas systems have a unique mode of interference, involving crRNA-guided recognition of nascent RNA and leading to DNA and RNA degradation. How type III systems acquire new CRISPR spacers is currently not well understood. Here, we characterize CRISPR spacer uptake by a type III-A system within its native host, Streptococcus thermophilus. Adaptation by the type II-A system in the same host provided a basis for comparison. Cas1 and Cas2 proteins were critical for type III adaptation but deletion of genes responsible for crRNA biogenesis or interference did not detectably change spacer uptake patterns, except those related to host counter-selection. Unlike the type II-A system, type III spacers are acquired in a PAM- and orientation-independent manner. Interestingly, certain regions of plasmids and the host genome were particularly well-sampled during type III-A, but not type II-A, spacer uptake. These regions included the single-stranded origins of rolling-circle replicating plasmids, rRNA and tRNA encoding gene clusters, promoter regions of expressed genes and 5 ' UTR regions involved in transcription attenuation. These features share the potential to form DNA secondary structures, suggesting a preferred substrate for type III adaptation. Lastly, the type III-A system adapted to and protected host cells from lytic phage infection.

Automated summary

This study characterized the uptake of CRISPR spacers by type III CRISPR-Cas systems within their native host, Streptococcus thermophilus. The results showed that Cas1 and Cas2 proteins are critical for type III adaptation, while genes responsible for crRNA biogenesis or interference do not significantly affect spacer uptake patterns. Type III spacers are acquired in a PAM- and orientation-independent manner, and certain regions of plasmids and the host genome are preferentially sampled during type III adaptation. Additionally, the type III system can adapt to and protect host cells from lytic phage infection.