Prophages are associated with extensive CRISPR-Cas auto-immunity

Abstract

CRISPR-Cas systems require discriminating self from non-self DNA during adaptation and interference. Yet, multiple cases have been reported of bacteria containing self-targeting spacers (STS), i.e. CRISPR spacers targeting protospacers on the same genome. STS may reflect potential auto-immunity as an unwanted side effect of CRISPR-Cas defense, or a gene regulatory mechanism. Here we investigated the incidence, distribution, and evasion of STS in over 100,000 bacterial genomes. We found STS in all CRISPR-Cas types and in one fifth of all CRISPR-carrying bacteria. Notably, up to 40% of I-B and I-F CRISPR-Cas systems contained STS. We observed that STS-containing genomes almost always carry a prophage and that STS map to prophage regions in more than half of the cases. Despite carrying STS, genetic deterioration of CRISPR-Cas systems appears to be rare, suggesting a level of tolerance to STS by other mechanisms such as anti-CRISPR proteins and target mutations. We propose a scenario where it is common and perhaps beneficial to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition in type I systems, without detrimental autoimmunity effects. The mechanisms of auto-immunity evasion create tolerance to STS-targeted prophages, and contribute both to viral dissemination and bacterial diversification.

CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa

“…Blastn hits with at least 95% sequence identity to a spacer and at least 95% sequence coverage were accepted as predicted spacer targets [18]. All spacers were blasted against their source genome to identify self-targeting spacers, as described in Nobrega et al [69], and using the previously defined blastn spacer search parameters.…”

“…CRISPR-Cas and self-targeting spacers is found across bacterial genomes [69]. The preservation of CRISPR-Cas systems in these genomes suggests cryptic mechanisms may exist that can protect bacteria from the detrimental effects of self-targeting auto-immunity.…”

PAM-repeat associations and spacer selection preferences in single and co-occurring CRISPR-Cas systems

“…There is evidence for some CRISPR-Cas functioning beyond adaptive immunity [24,25]; however, even within the context of an adaptive immune system, CRISPR-Cas systems can serve different roles (e.g., as the first line of defense or as an activator of other immune system pathways). This can be a reason why 23% of genomes with CRISPR-Cas systems contain more than one subtype [26], despite their costs [27,28]. There are preferred combinations of certain subtypes, suggesting that there is an added benefit of having a specific combination of different subtypes present in the cell.…”

Members of a highly widespread bacteriophage family are hallmarks of metabolic syndrome gut microbiomes

“…We predicted CRISPR arrays among the bacterial contigs using CRISPRdetect v2.4 91 (option array_quality_score_cutoff 3) and used these to match bacterial contigs and phage contigs. In addition, we used a dataset of 1,473,418 CRISPR spacers that had previously been predicted 62,92 in genomes contained in the Pathosystems Resource Integration Center (PATRIC) 93 database to match to phage contigs with spacePharer v2-fc5e668 94 using standard settings and cutoffs. This process resulted in 3,727 spacer hits, of which 2,244 hits were either to PATRIC genomes or to bacterial contigs from this study with definite CAT classifications at the phylum level ( Supplementary Table 3 ).…”