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Thanks to the greater availability of prokaryotic genome sequences, bioinformatic analysis has revealed that CRISPR systems are extremely abundant in prokaryotes, with roughly 40% of bacterial and over 85% of archaeal species harboring these systems (Makarova et al. 2019). This diversity, conferred by the remarkable variety of the Cas protein sequences, gene composition, and architecture of the loci, underpins the differences in how each of the three phases of adaptive immunity is performed. CRISPR systems have not only evolved to use different types of nucleic acids (DNA, RNA, or both) as a substrate (Marraffini and Sontheimer 2008; Hale et al. 2009; Kazlauskiene et al. 2016), but also can target different modalities (i.e. single‐ or double‐stranded) (Ma et al. 2015; Strutt et al. 2018) and a wide spectrum of different genomic sequences, thanks to diverse PAM requirements (Mojica et al. 2009; Gasiunas et al. 2020).

The origin and evolution of CRISPR systems are complex, but it seems that they have originated by domesticating various components of mobile genetic elements and subsequent integration with the “antediluvian” prokaryotic toxin–antitoxin defense systems (Koonin and Makarova 2019). The module of genes responsible for the adaptation phase is thought to originate from a class of transposons carrying a homologue of cas1 gene, collectively named casposons, while the CRISPR array is thought to originate from the inverted repeats flanking the casposon. The effector module seems to have evolved from a transposon‐encoded nuclease able to target DNA and RNA, which through a putative series of duplication and subsequent deletions lead to the current collection of effector enzymatic activities (Makarova et al. 2019; Koonin and Makarova 2019).

Importantly, the diversity of Cas systems across species also translates into how these systems can be used as a tool, where one can choose the most suitable CRISPR system for their target (DNA or RNA), a sequence of choice (by choosing a Cas protein with a pertinent PAM) or application (by choosing a Cas system with the desired outcome). To fully explore this untapped potential of the microbial CRISPR systems, significant efforts to establish a robust classification of CRISPR‐Cas systems have been made over the past decade. As there are no universally present cas genes that could act as an identifying trait, CRISPR classifications have been based on multiple factors, mainly on comparison of genomic loci organization and gene repertoires involved in a particular system. The most up‐to‐date classification is used in this chapter (Makarova et al. 2019).

All CRISPR‐Cas systems can be divided into two distinct classes based on the organization of the effector complex (Figure 3.2). In class 1 systems, the effector complex is composed of multiple Cas proteins, where individual subunits are needed for binding crRNA and recognition of the target nucleic acids, unwinding, and nucleolytic degradation. In contrast, class 2 systems contain a single multidomain protein, which catalyzes all of the activities necessary for the interference phase. Each of the classes can then be further divided into six types (I–VI) based on the organization of individual cas genes into functional modules, and then further classified into subtypes. Cas gene nomenclature also reflects their classification: currently, the set of cas genes involved in adaptation or crRNA biogenesis are denoted as cas1‐11 and are shared across different types. In contrast, the names of effector cas genes are reserved for specific types – for example, type II uses Cas9, type V uses Cas12, and type VI Cas13. Subtypes are further specified by suffices, such as Cas12a, Cas12b, Cas12c, and so on; however, as many on the genes also have older familiar names (e.g. Cpf1 is the original name for Cas12a), these will be mentioned where appropriate as a point of reference. The ancillary genes continue to be referred to by their legacy names (e.g. Csm6).

While the interference module is the prominent feature in the classification of CRISPR systems, each of the classes and types also differ mechanistically in the manners of crRNA biogenesis and acquisition of spacers. The traits of main CRISPR‐Cas systems will be discussed, with some differences between different subtypes touched upon as well; however, the intricacies and finesses of further classification are beyond the scope of this Chapter and the reader is invited to consult recent excellent reviews on the topic (Hille et al. 2018; Koonin and Makarova 2019; Makarova et al. 2019; Nussenzweig and Marraffini 2020).