Edited by Joel M. Gottesfeld Prokaryotes deploy CRISPR-Cas-based RNA-guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems, such as type I-E, are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-Especific extended C-terminal tail of Cas1-displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli. Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in a few CRISPR-Cas variants, such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.Prokaryotes utilize an adaptive immune response mediated by CRISPR and CRISPR-associated proteins (Cas) 2 to respond to infections by mobile genetic elements (MGE) (viz. phages and plasmids) (1-4). CRISPR encompasses a typical architec-This work was supported by Department of Biotechnology (DBT) Grants BT

During CRISPR adaptation, short sections of invader derived DNA of defined length are specifically integrated at the leader-repeat junction as spacers by Cas1-2 integrase complex. While several variants of CRISPR systems utilise Cas4 as an indispensible nuclease for processing the PAM containing prespacers to a defined length for integration-surprisingly-a few CRISPR systems such as type I-E are bereft of Cas4.Therefore, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. In Escherichia coli, we show that Cas1-2/I-E-via the type I-E specific extended C-terminal tail of Cas1 -displays intrinsic affinity for PAM containing prespacers of variable length and its binding protects the prespacer boundaries of defined length from the exonuclease action that ensues the pruning of aptly sized substrates for integration. This suggests that cooperation between Cas1-2 and cellular exonucleases drives the Cas4 independent prespacer capture and processing in type I-E. KEYWORDSPrespacer processing, CRISPR adaptation, Protospacer adjacent motif, Cas1-Cas2, Prespacer integration 2 3 DATA AVAILABILITYReads obtained from high-throughput sequencing have been deposited in the Sequence Read Archive (SRA) under accession number: PRJNA527928.