Identification of regulatory sequences in Aca11 and Aca13 for detection of anti-CRISPR and protein–protein interaction

Anti-CRISPR (Acr) proteins are frequently co-encoded with the anti-CRISPR associated (Aca) proteins, which act as repressors for regulating Acr expression within acr-aca operons. We previously identified three aca genes (aca11-13) from Streptococcus mobile genetic elements, but their regulatory mechanisms remained unclear. Here, we showed that Aca11 and Aca13 mediate bidirectional regulation in acr-aca operons through recognition of their inverted repeat (IR) sequences within the acr promoters. Based on the bioinformatics search using Aca13 with its IR sequences, we discovered a novel type II-A Acr (named AcrIIA35). AcrIIA35 exhibits a potent inhibitory activity against St1Cas9 by interfering with DNA recognition of Cas9 in bacterial and human cells. We also developed a novel Aca-driven protein-protein interaction detection (APID) system by integrating Aca-tagged target proteins with fluorescently labeled IR-DNA probes. The APID system enables efficient detection of protein-protein interaction using proteins or crude cell lysates. Utilizing the APID system, we have further elucidated the mechanism of AcrIIA24, which can interact with the HNH nuclease domain of St3Cas9 to inhibit the DNA cleavage activity of Cas9. Collectively, our work expands the understanding of Aca functions to modulate Acrs and expands the potential for Aca-based applications in CRISPR technologies.