NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

NanoPAMDA enabled rapid, time-resolved kinetic PAM profiling of 14 metagenome-derived Cas9 candidates, and one effector, E10, showed PAM-specific activity in vitro.

• Why it matters: CRISPR-Cas9 orthologs are still functionally underexplored, even as metagenomic sequencing data grows, creating a need to discover and characterize PAM preferences at scale.
• What they did: A multi-stage computational pipeline screened 660,185 metagenome-assembled genomes from 17 catalogs plus de novo human microbiome reads, yielding 14 candidates for NanoPAMDA testing.
• The result: NanoPAMDA’s Nanopore long-read adaptation supported parallel PAM determination, and E10 was catalytically active in Escherichia coli, enabling scalable discovery-to-biochemistry workflows.

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