Exploring the deletion landscape of S. aureus Cas9 with SABER

Profiling tolerated amino acid deletions in proteins can elucidate structure-function relationships, reconstruct intermediate stages in protein evolution, and be used to engineer minimized versions of proteins with size-sensitive biotechnology applications. Despite advances in deletion library construction techniques over the past several decades, there are presently few methods available that are simultaneously efficient, precise, and easy to implement. Here we present SABER, a novel approach which utilizes SpRYCas9, a near-PAMless engineered SpCas9 variant, as a molecular biological tool for building deletion libraries with unprecedented speed and ease. We applied this technique to the small and structurally divergent Cas9 from Staphylococcus aureus (SaCas9) and mapped the set of deletions tolerated for DNA binding activity. We proceeded to use this information to design a set of minimal SaCas9-based effectors capable of CRISPRi transcriptional repression in bacterial cells. Our findings provide new insights into the function of certain structural elements in SaCas9, and we anticipate that our dSaCas9 deletion map may prove useful in further efforts to develop minimal Cas9-based effectors and gene editors.