Deep mutational scanning identifies variants of Cas1 and Cas2 that increase spacer acquisition in type II-A CRISPR-Cas systems

A remarkable feature of CRISPR-Cas systems is their ability to acquire short sequences from invading viruses to create a molecular record of infection. These sequences, known as spacers, are inserted into the CRISPR locus by the Cas1-Cas2 integrase complex and mediate sequence- specific immunity in prokaryotes. Spacer acquisition has been used to develop unique biotechnological applications such as the immunization of industrially relevant bacteria against bacteriophage infection and the recording of biological signals into stable genetic information. These technologies, however, are constrained by the low efficiency of the spacer acquisition process. To overcome this limitation, we developed a genetic system that combined deep mutational scanning (DMS) of cas genes from the Streptococcus pyogenes type II-A CRISPR- Cas system with a method that selects bacteria that acquire new spacers. This procedure enabled the identification of cas mutations that support up to a sevenfold increase in the levels of spacer acquisition and a significant enhancement of immunity against phage infection. In addition, our analysis revealed key interactions at the Cas1-Cas2 interface critical for spacer integration. Our findings provide insights into the molecular determinants of spacer acquisition and offer a platform to improve CRISPR-Cas-based applications.