Commentary: Type I CRISPR-Cas targets endogenous genes and regulates virulence to evade mammalian host immunity

Citation: Müller-Esparza H and Randau L (2017) Commentary: Type I CRISPR-Cas targets endogenous genes and regulates virulence to evade mammalian host immunity. Type-I CRISPR-Cas systems are abundant antiviral defense systems of bacteria and archaea. The hallmark sequences of these systems are short CRISPR RNAs (crRNAs) that contain spacer sequences which guide an interference complex termed Cascade (CRISPR-associated complex for antiviral defense) toward their viral DNA target (van der Oost et al., 2014). In the recent years, several subtypes of this Type I CRISPR-Cas system have been studied in detail and all interference complexes share a central crRNA whose spacer is protected by a multi-subunit filament of Cas7 (Csy3) backbone proteins (Gleditzsch et al., 2016). The termini of the CRISPR RNA are capped by Cas5 (Csy2) and Cas6 proteins and additional large and small subunits can mediate interactions with the target DNA, i.e., the protospacer and the protospacer-adjacent motif (PAM). The crRNA spacer is used to scan DNA for complementary bases and the large subunit identifies PAM sequences to achieve self-versus non-self-discrimination and to avoid self-targeting. Finally, Cascade complexes recruit a helicase/nuclease, termed Cas3, to degrade identified DNAs (Hochstrasser et al., 2014). In a recent study in Cell Research (Li et al., 2016), Li et al., highlight a surprising deviation from these established concepts and show self-targeting of the lasR mRNA based on only nine nucleotide complementarity between the CRISPR RNA and the target mRNA, as well as the presence of a small " 5 ′-GGN-3 ′ " recognition motif. Earlier studies have indicated that Escherichia coli Type I-E Cascade can bind ssRNA in vitro (Jore et al., 2011) and that Cas3 can degrade ssRNA (Beloglazova et al., 2011). However, specific DNA targeting is considered to be essential for proper identification of foreign DNA elements while maintaining genome integrity. The described RNA targeting relies on a discrimination mechanism similar to the established DNA targeting pathway and suggests that a 5 ′-GGN-3 ′ PAM-like sequence must exist to mark the mRNA-target. However, a conventional PAM sequence in Type IF Cascade prevents base pairing between the 8 nt 5 ′-repeat-tag of the crRNA and the DNA target (Rollins et al., 2015), while the identified PAM-like sequence in the lasR mRNA would prevent base pairing with the 3 ′-tag (Figure 1A). This implies that Cascade would have evolved a specific RNA target discrimination mechanism. The 3 ′-tag of a crRNA is bound by Cas6f …