Abstract
Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. We report that non-homologous end-joining (NHEJ) and type II-A CRISPR-Cas systems only co-occur once among 5563 fully sequenced prokaryotic genomes. We investigated experimentally the possible molecular interactions using the NHEJ pathway from Bacillus subtilis and the type II-A CRISPR-Cas systems from Streptococcus thermophilus and Streptococcus pyogenes. Our results suggest that the NHEJ system has no effect on CRISPR immunity. On the other hand, we provide evidence for the inhibition of NHEJ repair by the Csn2 protein. Our findings give insights on the complex interactions between CRISPR-Cas systems and repair mechanisms in bacteria, contributing to explain the scattered distribution of CRISPR-Cas systems in bacterial genome.
Highlights
Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation
The non-homologous end-joining (NHEJ) pathway was present in 24.7% and the type II CRISPR-Cas system in 6.9% of the genomes, and these systems were very unevenly distributed among bacterial phyla (Supplementary Fig. 1 and Supplementary Table 1)
Firmicutes and Proteobacteria were the only phyla with genomes encoding enough type II CRISPR-Cas systems and NHEJ, to perform robust statistical analyses (Supplementary Fig. 1)
Summary
Type II CRISPR-Cas systems introduce double-strand breaks into DNA of invading genetic material and use DNA fragments to acquire novel spacers during adaptation. These breaks can be the substrate of several DNA repair pathways, paving the way for interactions. DSB can be repaired either by homologous recombination (HR) or by non-homologous end-joining (NHEJ) These mechanisms could affect the efficiency of CRISPR-Cas interference by repairing the breaks. In type II-A CRISPR-Cas systems, Csn[2] binds and slides along free DNA ends in the same manner as the Ku protein of the NHEJ system[28,31,32,33,34]. If Cas proteins and proteins involved in DNA repair mechanisms recognize the same substrate, a competition might arise leading to antagonistic interactions between the two processes
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