An updated evolutionary classification of CRISPR–Cas systems

Abstract

The evolution of CRISPR–cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR–cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR–Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

“…These links were probably not detected due to low estimated genome completion in some samples. Based on a recent paper 50 , we classified CRISPR-Cas modules by manually examining the operon architectures of annotated contigs. Although we cannot determine whether a particular viral contig was in a virulent/lytic state at the time of sampling, in the input and day 7 samples, the contigs with the highest read coverage, identified as viral by the above criteria, had coverage several-fold higher than the most abundant bacterial or archaeal contig (input, 5.1-fold higher; T7, 4.0-fold higher), suggesting these viruses were virulent at the time of sampling.…”

New CRISPR–Cas systems from uncultivated microbes

“…3a) suggests that this archaeal CRISPRCas system does not clearly fall into any existing type II subtype. The presence of cas4, affiliate it with type II-B systems 3,11 , yet the Cas9 sequence is more similar to type II-C proteins (Extended Data Fig. 4, Supplementary Data 3).…”

“…One of the hallmarks of CRISPR-Cas9 (type II) systems was their presumed presence only in the bacterial domain 3,11 . We were therefore surprised to discover Cas9 proteins encoded in genomes of the nanoarchaea ARMAN-1 (Candidatus Micrarchaeum acidiphilum ARMAN-1) and ARMAN-4 (Candidatus Parvarchaeum acidiphilum ARMAN-4) 12,13 in acid-mine drainage (AMD) metagenomic datasets (Extended Data Table 1 and Extended Data Fig.…”

“…A sensitive search using profile Hidden Markov Models (HMMs) 34 built from published Cas proteins 3,4 indicated that four of the six CasY proteins had local similarities (e-values 4×10 −11 -3×10 −18 ) to C2c3 in the C-terminal region overlapping the RuvC domains and a small region (~45 aa) of the N-terminal region (see Extended Data Fig. 3c).…”

Advancing biotechnology with CRISPR/Cas9: recent applications and patent landscape

“…only a single crRNA-effector enzyme and no tracrRNA part is required for cutting DNA. It differs from it by possessing a specific RNA processing domain that allows to process the crRNA into multiple gRNAs [55,69,92,101]. Finally, the gRNA scaffold can be extended to include effector protein recruitment stem-loops, which has been shown to enhance transcriptional regulation [8,44,100] (Fig.…”