Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

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.

Primed acquisition and microhomology-mediated end-joining cooperate to confer specific CRISPR immunity against invasive genetic elements

“…Error-prone repair systems contributing to avoid CRISPR self-targeting could be widespread in bacteria. For example, the non-homologous end-joining (NHEJ) pathway is co-present with the CRISPR-Cas system in some bacterial species 40,41 . However, the NHEJ system has no effect on CRISPR immunity when both NHEJ genes and CRISPR-Cas subtype II-A system were co-expressed in a heterogeneous host 40 .…”

Ecology Shapes Microbial Immune Strategy: Temperature and Oxygen as Determinants of the Incidence of CRISPR Adaptive Immunity

“…Previous analyses have shown that bacterial thermophiles 16 and archaea (both mesophilic and thermophilic) frequently have CRISPR sys-17 tems (∼ 90%), whereas less than half of mesophilic bacteria have CRISPR 18 (∼ 40%; [8,9,10,11,12]). Environmental samples have revealed that many 19 uncultured bacterial lineages have few or no representatives with CRISPR sys- 20 tems, and that the apparent lack of CRISPR in these lineages may be linked 21 to an obligately symbiotic lifestyle and/or a highly reduced genome [13]. Nev- 22 ertheless, no systematic exploration of the ecological conditions that favor the 23 evolution and maintenance of CRISPR immunity has been made.…”

“…37 [19,20]). More recently it has been shown that at least one CRISPR-associated 38 (Cas) protein can suppress non-homologous end-joining (NHEJ) DNA repair, 39 which may lead to selection against having CRISPR in some taxa [21]. In or- 40 der to determine the relative importances of these different mechanisms, we 41 must first identify the habitats and microbial lifestyles associated with CRISPR 42 immunity.…”

“…Recently, Bernheim et al [21] demonstrated that the type II-A CRISPR system 209 interferes with the NHEJ DNA repair pathway, leading to an inverse relationship 210 between the presence of type II-A systems and the NHEJ pathway in microbial 211 genomes. We hypothesized that this negative relationship between CRISPR and 212 NHEJ might be more widespread across system types.…”

“…Possibly, this association can be 296 explained by inhibitory effects of CRISPR on NHEJ DNA repair. Type II-A 297 CRISPR systems have been shown to directly interfere with the action of the 298 NHEJ DNA repair pathway in prokaryotes [21]. Reactive oxygen species are 299 produced during aerobic metabolism and can cause DNA damage [32], making 300 NHEJ potentially particularly important in aerobes.…”