Rational and computation-assisted engineering of a compact and efficient StaCas9 genome editor

Type II-A CRISPR-Cas9 nucleases are widely used for genome editing, yet their functional diversity and therapeutic potential remain incompletely explored. In this study, we systematically analyzed natural variation in PAM recognition among SaCas9 orthologs and identified StaCas9 as a compact and efficient nuclease recognizing an NNG PAM. Structural and sequence analyses revealed that S983 within the PAM-interacting domain contributes to the PAM preference of StaCas9. StaCas9 enabled efficient genome editing across multiple endogenous loci in human cells and achieved high-efficiency disruption of the therapeutically relevant PCSK9 gene, supporting its potential for gene therapy. Furthermore, guided by structural insights, we significantly enhanced the editing activity of StaCas9. Together, these results expand our understanding of PAM recognition in type II-A Cas9 nucleases and establish StaCas9 as a high-performance genome-editing tool for therapeutic applications.