to cleave the nontarget strand, and then the target strand (Jeon et al. 2018), generating a staggered DNA cut with 4–5 nt long 5’ overhangs between the 18th and 23rd base from the PAM (Zetsche et al. 2015). After successful cleavage, Cas12a releases the PAM‐distal DNA fragment but continues to bind to the PAM‐proximal fragment (Figure 3.5b). Crucially, crRNA remains bound to the target strand, allowing the enzyme to remain in catalytically active state. This allows Cas12a proteins to exhibit an indiscriminate nuclease activity on any ssDNA it may encounter (Chen et al. 2018). This activity might be important for the complete clearance of invading genomes. Importantly, the indiscriminate ssDNase activity has been reported for many Cas12 proteins: Cas12b (Li et al. 2019a), Cas12f (Harrington et al. 2018), and Cas12c, ‐h, ‐i, and g (Yan et al. 2019). Furthermore, Cas12g was shown recently to be able to target RNA molecules, and to pose indiscriminate cleavage of ssDNA and ssRNA. Many type II proteins can target both ssDNA and dsDNA (Ma et al. 2015).
Figure 3.5 Interference mechanisms in class 2 systems. Representative mechanisms of the most commonly used class 2 systems are depicted here. In (a), Cas9:crRNA:tracrRNA binds to the target sequence, activating the RuvC and HNH nuclease domain to generate a blunt double‐stranded DNA break proximal to PAM site. In (b), Cas12a complexed with its cognate crRNA recognized target sequence, inducing cleavage of nontarget strand by its single RuvC domain. The enzyme then rearranges to cleave the target strand, releasing the PAM‐distal DNA fragment. The enzyme remains active as it still binds activating PAM‐proximal sequence, exhibiting collateral activity on any ssDNA able to enter the active site. (c) depicts a general mechanism of Cas13 enzymes, able to target RNA by base pairing with its crRNA. Upon recognition of target RNA, Cas13 enzyme undergoes a major conformational change that assembles a composite HEPN domain, exhibiting indiscriminate ssRNA nucleolytic cleavage. Activated Cas13 is therefore able to degrade the target RNA molecule, but also any bystander RNA. Sites of DNA cleavage activity are depicted by orange arrows and RNA cleavage by red arrowheads.
Furthermore, type V systems also contain a collection of heterogeneous and poorly characterized subtype V‐U; these systems typically lack the adaptation module and contain much smaller effector proteins, making them unlikely to be functional. However, follow‐up studies have identified interference functions with some, prompting their upgrade to a separate type V‐F (Harrington et al. 2018). Finally, an unusual group of what are now Cas12k proteins have been experimentally shown to interact with a bacterial transposase and promote transposon integration through a crRNA‐guided mechanism (Strecker et al. 2019b); this is likely to reflect the proposed evolutionary trajectory of CRISPR systems, proposed to originate as machinery important for transposition (Makarova et al. 2019).
3.3.2.2.3 Type VI
The most recently fully characterized CRISPR systems belong to type VI (Meeske et al. 2019). Similar to other class 2 proteins, the type VI effector Cas13 (with representative Cas13a and Cas13b) also forms a bilobed structure with the crRNA accommodated in its central cleft (Liu et al. 2017b; Liu et al. 2017c; Slaymaker et al. 2019). Unlike Cas9 and Cas12 effectors, Cas13 lacks DNase domains such as HNH or RuvC, but contains two HEPN domains, often found in RNases (Shmakov et al. 2017; Makarova et al. 2019), allowing this enzyme to target ssRNA (Abudayyeh et al. 2016; East‐Seletsky et al. 2016; Smargon et al. 2017; Zhang et al. 2018). Additionally, Cas13 proteins contain an alpha‐helical domain intuitively called Helical‐1 domain, which together with HEPN‐2 domain participates in pre‐crRNA processing. Binding of pre‐crRNA in the central channel of Cas13 leads to a conformational change that activates the Helical‐1 domain, stimulating it to incise the pre‐crRNA generating a mature crRNA (typically with 28–30 nt spacer and 30 nt long hairpin) (East‐Seletsky et al. 2016). The structure of the crRNA differs between two prominent subcategories, with the hairpin‐forming repeat sequence being at the 5’ or 3’ end of the spacer in Cas13a or Cas13b processed RNA, respectively (East‐Seletsky et al. 2016; Slaymaker et al. 2019).
Recognition of the target RNA bears similarity to other CRISPR systems (Figure 3.5c). The pairing between the crRNA and target RNA at the central seed sequence is essential for binding and then stimulating RNase activity (Abudayyeh et al. 2016; Tambe et al. 2018), whereas peripheral mismatches are tolerated to a greater extent. Further elements are also needed for activation of RNase activity of the HEPN domains. Sequence and structure of the hairpin are critical, where reducing the length under 24 nt or mutating key nucleotides significantly decreased its activity (Abudayyeh et al. 2016; Smargon et al. 2017). Analogous to PAM, Cas13 also requires protospacer flanking site (PFS) proximal to the target site; the exact sequence and position is dependent on the subtype and species. For example, Cas13a requires a 3’ non‐G PFS, while Cas13b need a PFS at either side of the protospacer, with the 5’ being depleted of C and the 3’ PFS having a consensus sequence of NAN or NNA, where N is any nucleotide (Abudayyeh et al. 2016, Smargon et al. 2017).
Productive base pairing between crRNA and target RNA triggers a conformational change bringing both of the HEPN domains in close proximity and assembling into a composite catalytic site on the outer surface of the protein (Liu et al. 2017b; Liu et al. 2017c). Activated HEPN domains can indiscriminately degrade ssRNA, both the target at single‐stranded regions and any other RNA in the vicinity (Abudayyeh et al. 2016; East‐Seletsky et al. 2016). This indiscriminate RNase activity was shown to be able to restrict invasion of RNA phages, such as MS2 (Abudayyeh et al. 2016). Furthermore, a recent study showed that type VI systems can confer immunity to DNA phages as well. Similarly to type III systems, indiscriminate RNase activity of Cas13 is able to induce growth arrest of the infected cells. While the growth arrest induced by type III systems is transient as Csm6 (which also contains HEPN domains) gets deactivated, Cas13 does not (likely due to persistent transcription from the phage genome, which remains intact), consequentially inducing dormancy. This way, the further expansion of the phage is prevented, achieving immunity on a population level (Meeske et al. 2019).
3.3.3 Adaptation
The last phase of the CRISPR‐mediated immunity that shall be addressed here is the adaptation phase, also known as spacer acquisition. In this phase, the memory of previous infections is recorded, allowing an organism and its descendants to confer immunity to the reinvading genome. The CRISPR array acts as a genetic ledger, with spacers acting as records of infections (with the most recent usually located closest to the leader sequence). The key players in spacer acquisition are Cas1 and Cas2, present in nearly every CRISPR system. In contrast to the ubiquity of these genes, understanding of molecular mechanisms of adaptation is restricted just to type I and type II systems with many mechanistic details still missing, with more studies needed to elucidate this process in its entirety.
The acquisition of spacers upon the invasion of an infectious genome that the host has not encountered before is often termed naïve spacer acquisition. This is an incredibly rare event, estimated to occur with a frequency of 10−7 per infected cell (Hynes et al. 2014; Heler et al. 2015). The acquisition of spacers by Cas1:Cas2 adaptation complex in these circumstances can be viewed as accidental, as it relies on other systems to generate suitable substrate for this protein. In E. coli, spacer acquisition was linked to excessive replication of the viral or plasmid genome, during which the inherently unstable replication intermediates are recognized and digested by the RecBCD endonuclease complex (involved in restriction and recombination), generating small fragments that can be captured and further processed by the adaptation complex (Levy et al. 2015). A similar mechanism has been described in Gram‐positive species as well, where the AddAB restriction system is able to enrich for spacers (Figure
