Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids

Abstract

CRISPR–Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites. In contrast to all other types of CRISPR–Cas systems, type IV has remained largely overlooked. Here, we describe a previously uncharted diversity of type IV gene cassettes, primarily encoded by plasmid-like elements from diverse prokaryotic taxa. Remarkably, via a comprehensive analysis of their CRISPR spacer content, these systems were found to exhibit a strong bias towards the targeting of other plasmids. Our data indicate that the functions of type IV systems have diverged from those of other host-related CRISPR–Cas immune systems to adopt a role in mediating conflicts between plasmids. Furthermore, we find evidence for cross-talk between certain type IV and type I CRISPR–Cas systems that co-exist intracellularly, thus providing a simple answer to the enigmatic absence of type IV adaptation modules. Collectively, our results lead to the expansion and reclassification of type IV systems and provide novel insights into the biological function and evolution of these elusive systems.

CRISPRCasTyper: An automated tool for the identification, annotation and classification of CRISPR-Cas loci

“…CRISPRCasTyper was compared with the widely used CRISPRCasFinder (Couvin et al 2018) using the manually curated CRISPR-Cas loci from Makarova et al 2020(Makarova et al 2020 , the newest type IV classification from Pinilla-Redondo et al 2019(Pinilla-Redondo et al 2019) and manually curated III-E loci (see Methods and Materials). We find that CRISPRCasTyper outperforms CRISPRCasFinder at identifying 17 subtypes and is equally accurate in the prediction of the remaining 2 subtypes included in CRISPRCasFinder (Fig.…”

“…Multi-systems and partial systems were excluded from the benchmark. Type IV loci were obtained from Pinilla-Redondo et. al.…”

“…While recent years have seen an extraordinary expansion in the classification of newly discovered systems, the current classification is predicted to be nearly complete at the "type" level (Makarova, Wolf, and Koonin 2018;Makarova et al 2020) . For a summary of the state of the art classification and nomenclature, we refer the readers to recent comprehensive reviews and articles (Makarova et al 2020;Pinilla-Redondo et al 2019) .…”

“…Here we present CRISPRCasTyper, a new tool that can accurately identify and annotate CRISPR and cas loci automatically based on the newest classification (Makarova et al 2020;Pinilla-Redondo et al 2019). Besides classifying cas operons, CRISPRCasTyper can also accurately assign subtypes to CRISPR arrays based on the sequence composition of the consensus repeat.…”

“…The increasing demand for bioinformatic tools that systematically detect and classify CRISPR-Cas systems has been largely challenged by their complex dynamic nature and rapidly expanding classification. Here, we developed CRISPRCasTyper, a new automated software tool with improved capabilities for identifying and typing CRISPR arrays and cas loci across prokaryotic sequences, based on the latest classification and nomenclature (39 subtypes/variants) (Makarova et al 2020;Pinilla-Redondo et al 2019) . As a novel feature, CRISPRCasTyper uses a machine learning approach to subtype CRISPR arrays based on the sequences of the direct repeats.…”