Figure 1: Comparison of Type I (left) and Type II (right) CRISPR-Cas interference mechanisms.

CRISPR arrays, comprised of direct repeats (DRs; royal blue and dark green) and spacer tags (light blue and light green) are first transcribed into a single large pre-crRNA by a promoter located within the CRISPR leader (lead). The resulting transcript is cleaved and processed into individual mature crRNAs by the Cas6 endonuclease (Type I systems) or the ubiquitous RNase III enzyme (Type II systems). Processing is mediated by characteristic secondary structures (hairpins) formed by Type I pre-crRNAs or by a trans-activating RNA (tracrRNA; brown) possessing homology to direct repeat sequences in Type II systems. A single synthetic guide RNA (gRNA) can replace the dual crRNA-tracrRNA interaction (not shown). Mature crRNAs are guided to invading nucleic acids through homology between crRNAs and the corresponding invader protospacer sequence. Type I interference requires the multiprotein Cascade complex (comprised of cas6-cas8b-cas7-cas5 in Clostridium difficile⁶² and C. pasteurianum), encoded downstream of the Type I CRISPR array. Type I and II interference mechanisms require recognition of one of multiple protospacer adjacent motif (PAM) sequences, which collectively comprise the consensus PAM element (red). The location of the PAM and the site of nucleolytic attack relative to the protospacer sequence differs between Type I and II CRISPR-Cas systems. Representative PAM sequences from C. difficile (Type I-B)⁶² and Streptococcus pyogenes (Type II)²⁵ CRISPR-Cas loci are shown. Nucleolytic attack by Cas3 or Cas9 results in a DNA nick (DN) or blunt double-stranded DNA break (DB), respectively. Both CRISPR-Cas loci contain cas1 and cas2 genes (not shown), while the Type I and II loci also contain cas4 and csn2 genes, respectively (not shown).