Cas9 senses CRISPR RNA abundance to regulate CRISPR spacer acquisition

Prokaryotes adapt to viral challenges by acquiring CRISPR memories from invaders through a process called adaptation. Previous study showed that this process requires Cas9 complexed with its RNA partners in type II-A system. How Cas9 functions in adaptation in other type II systems is poorly understood. Here using type II-C system of N. meningitidis and meningococcal disease associated filamentous phage MDAF as model, we show that RNA free apoCas9 dramatically enhances adaptation efficiency and that tracrRNA and crRNA together repress rather than enhance adaptation through interacting with Cas9. We also discovered that a Cas9 lacking the recognition lobe can no longer be suppressed by its RNA partners. We demonstrate how this interplay between Cas9 and its RNA partners benefit the host bacteria by regulating adaptation during CRISPR neo-genesis and CRISPR array collapse. We further show that this regulation is a conserved process in type II-C systems. Our results uncover a brand-new adaptation regulation mechanism and demonstrate the first biological function of RNA-free apoCas9. Overall design: MDA phage treated Neisseria meningitidis strains with genetic manipulation of CRISPR-Cas system components.