CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

Abstract

Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein-binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap.

Figure 1.

The CRISPRmap tree: a map of repeat sequence and structure conservation. The hierarchical tree is generated with respect to repeat sequence and structure pairwise similarity and the branches are coloured according to their occurrence in the domains bacteria (dark brown) or archaea (blue-green). The rings annotate the conserved structure motifs (inner), sequence families (middle) and the superclass (outer). Motifs and families are marked and highlighted with yellow circles, and grey squares, respectively. Finally, we marked locations of published CRISPR-Cas systems for which experimental evidence of the processing mechanism exists (13,17–25,33–36,51). A summary for these published systems is given in Supplementary Table S20. Repeats that show no conservation, i.e. were not assigned to either a sequence family or structure motif, were removed to clarify the visualisation.

Figure 2.

CRISPRs cluster into six major superclasses according to sequence and structure similarity. We summarised general results of our structure motif detection (i.e. structured or unstructured), Cas-subtype annotations (10) and taxonomic phyla beside each superclass.

Figure 3.

Highlighting the advantage of independent clustering approaches. (A) CRISPRs in the largest sequence family, F1, are mostly unstructured; however, for 50 CRISPRs also a conserved structure motif, M10, was identified. This indicates that subsets of conserved families can be structured. F1 contains the conserved 5′ tag, marked with the magenta box. (B) Structure motif M28 shows no sequence conservation, but a conserved structure (base pairs are highlighted in yellow). The many compensatory base pairs are marked in the alignment with squares. This structure has been verified via mutational analyses in (20). Potential cleavage sites are indicated as observed in the literature (13,17–21,23–25,33–36).

Figure 4.

Relative ratios of Cas1 sequence clusters and Cas-subtype annotations per superclass. (A) Cas1 sequence clusters correspond well to the superclass and thus the CRISPRmap tree with the exception of superclass E; superclass E is diverse in both repeat and associated Cas1 conservation and it probably contains only partial data. (B) Bacterial CRISPRs that are assigned to well-defined structure motifs are associated with subtypes I-C, I-E and I-F in superclasses B–D and are strongly linked to both repeat and Cas1-sequence similarities (i.e. CRISPR evolution). Superclass A and F contain both bacterial and archaeal CRISPRs (many are unstructured), which are loosely associated with the remaining type I and both type III subtypes. These subtypes do not correspond to Cas1 and repeat evolution and are likely composed of interchangeable protein complexes or modules. The diversity of superclass E is also reflected by the mixture of all subtypes; in addition, the majority of type II CRISPRs are also located in this region.