Histones direct site-specific CRISPR spacer acquisition in model archaeon

In Pyrococcus furiosus, histones bind and bend DNA to enable integration of new spacer fragments into CRISPR loci. CRISPR-Cas systems provide heritable immunity against viruses and other mobile genetic elements by incorporating fragments of invader DNA into the host CRISPR array as spacers. Integration of new spacers is localized to the 5 & PRIME; end of the array, and in certain Gram-negative Bacteria this polarized localization is accomplished by the integration host factor. For most other Bacteria and Archaea, the mechanism for 5 & PRIME; end localization is unknown. Here we show that archaeal histones play a key role in directing integration of CRISPR spacers. In Pyrococcus furiosus, deletion of either histone A or B impairs integration. In vitro, purified histones are sufficient to direct integration to the 5 & PRIME; end of the CRISPR array. Archaeal histone tetramers and bacterial integration host factor induce similar U-turn bends in bound DNA. These findings indicate a co-evolution of CRISPR arrays with chromosomal DNA binding proteins and a widespread role for binding and bending of DNA to facilitate accurate spacer integration.

Automated summary

The histones in Pyrococcus furiosus play a crucial role in directing the integration of CRISPR spacers, ensuring accurate integration at the 5' end of the CRISPR array. This co-evolution of CRISPR arrays with chromosomal DNA binding proteins highlights the widespread role of DNA binding and bending in facilitating spacer integration.