Structure and engineering of miniature Acidibacillus sulfuroxidans Cas12f1

The miniature CRISPR-Cas12f nucleases allow for efficient delivery via cargo-size-limited adeno-associated virus delivery vehicles, thereby showing promising potential for in vivo therapeutic applications. Acidibacillus sulfuroxidans Cas12f1 (AsCas12f1, 422 amino acids) is the most compact Cas12f nuclease identified to date, showing a moderate level of genome-editing activity in human cells compared to Cas9 and Cas12a. Understanding the mechanisms of why such a compact nuclease is active for genome editing would facilitate its rational engineering. Here, we report the cryo-EM structure of the AsCas12f1-sgRNA-dsDNA ternary complex, and reveal that AsCas12f1 functions as an asymmetric dimer for single-guide RNA (sgRNA) binding and DNA targeting. The detailed mechanisms for dimer formation, PAM recognition, and sgRNA accommodation are elucidated. Leading by the structural knowledge, we extensively engineer the AsCas12f1 nuclease and its corresponding sgRNA, resulting in an evolved AsCas12f1-sgRNA combination with drastically enhanced genome editing activity in human cells. These results provide further understanding of compact CRISPR systems and expand the mini CRISPR toolbox for therapeutic applications.