Metagenomic discovery of CRISPR-associated transposons

Abstract

Significance CRISPR-Cas systems confer bacteria and archaea with adaptive immunity against mobile genetic elements. These systems also participate in other cellular processes. For example, CRISPR-associated Tn7 transposons (CASTs) have co-opted nuclease-inactive CRISPR effector proteins to guide their transposition. We bioinformatically survey metagenomic databases to uncover CASTs, including systems with new architectures and ones that use distinct CRISPR subtypes. We also describe a putative non-Tn7 CAST that co-opts Cas12. Our findings propose mechanisms for vertical and horizontal CAST targeting and shed light on how CASTs have coevolved with CRISPR-Cas systems. CRISPR-associated Tn7 transposons (CASTs) co-opt cas genes for RNA-guided transposition. CASTs are exceedingly rare in genomic databases; recent surveys have reported Tn7-like transposons that co-opt Type I-F, I-B, and V-K CRISPR effectors. Here, we expand the diversity of reported CAST systems via a bioinformatic search of metagenomic databases. We discover architectures for all known CASTs, including arrangements of the Cascade effectors, target homing modalities, and minimal V-K systems. We also describe families of CASTs that have co-opted the Type I-C and Type IV CRISPR-Cas systems. Our search for non-Tn7 CASTs identifies putative candidates that include a nuclease dead Cas12. These systems shed light on how CRISPR systems have coevolved with transposases and expand the programmable gene-editing toolkit.