Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back

Abstract

The Clustered Regularly Interspaced Palindromic Repeats (CRISPR)-CRISPR-associated proteins (Cas) systems of bacterial and archaeal adaptive immunity show multifaceted evolutionary relationships with at least five classes of mobile genetic elements (MGE). First, the adaptation module of CRISPR-Cas that is responsible for the formation of the immune memory apparently evolved from a Casposon, a self-synthesizing transposon that employs the Cas1 protein as the integrase and might have brought additional cas genes to the emerging immunity loci. Second, a large subset of type III CRISPR-Cas systems recruited a reverse transcriptase from a Group II intron, providing for spacer acquisition from RNA. Third, effector nucleases of Class 2 CRISPR-Cas systems that are responsible for the recognition and cleavage of the target DNA were derived from transposon-encoded TnpB nucleases, most likely, on several independent occasions. Fourth, accessory nucleases in some variants of types I and III toxin and type VI effectors RNases appear to be ultimately derived from toxin nucleases of microbial toxin-antitoxin modules. Fifth, the opposite direction of evolution is manifested in the recruitment of CRISPR-Cas systems by a distinct family of Tn7-like transposons that probably exploit the capacity of CRISPR-Cas to recognize unique DNA sites to facilitate transposition as well as by bacteriophages that employ them to cope with host defense. Additionally, individual Cas proteins, such as the Cas4 nuclease, were recruited by bacteriophages and transposons. The two-sided evolutionary connection between CRISPR-Cas and MGE fits the "guns for hire" paradigm whereby homologous enzymatic machineries, in particular nucleases, are shuttled between MGE and defense systems and are used alternately as means of offense or defense.

Keywords: CRISPR adaptation; CRISPR effector modules; CRISPR-Cas systems; casposons; mobile genetic elements.

Fig. 1.

—Current classification of CRISPR-Cas systems. The organization of the CRISPR-cas loci and domain architectures of the effector proteins as well as the (predicted) target (DNA or RNA, or both) are shown for each subtype. The trees reflect the latest classifications for the Class 1 and Class 2 CRISPR-Cas systems (Makarova etal. 2015; Koonin etal. 2017) and are not traditional phylogenetic trees. The block arrows represent cas genes (not to scale); homologous genes are shown by the same color. For each cas gene, the systematic name and the legacy name (if any) are indicated below the respective arrow. The adaptation and effector modules are shaded in blue and light brown, respectively. A shaded outline for an arrow depicting a gene indicates that the gene in question is present only in a subset of CRISPR-cas loci of the respective subtype. For subtype III-D, a locus with a reverse transcriptase fused to cas1 is included; other reverse transcriptase-containing variants, from subtypes III-A and III-D, are not shown. SS, small subunit; TM, predicted transmembrane segment.

Fig. 2.

—Contributions of mobile genetic elements to the origin and evolution of CRISPR-Cas systems: adaptation module and CRISPR. The block arrows show genes (not to scale); the gene organizations of the depicted genetic elements are shown schematically. The curved arrows show inferred ancestor–descendent relationships. The double black arrowheads represent CRISPR repeats (to emphasize their palindromic organization in many although not all CRISPR arrays). The diamonds represent spacers that are colored differently, to emphasize that these sequences are unique. Each CRISPR array is schematically shown as three repeats and two spacers although the actual size differs from such minimal units to hundreds of repeats and spacers. Abbreviations: CARF, CRISPR-Associated Rossmann Fold (domain); HEPN, Higher Eukaryote and Prokaryote Nucleotide-binding (domain). LE, left end; RE, right end; RT, reverse transcriptase; TIR, terminal inverted repeat. VapD is a toxin with the activity of an interferase, that is, an RNase that cleaves ribosome-associated mRNA.

Fig. 3.

—Contributions of mobile genetic elements to the origin and evolution of CRISPR-Cas systems: Class 2 effector proteins. The genes for Class 2 effector proteins and the homologous proteins encoded by transposons or toxin–antitoxin modules are shown by block arrows (roughly to scale). Different colors denote distinct domains or uncharacterized regions in the effector proteins. The curved arrows show putative ancestor–descendent relationships. RuvC I, II, III are distinct amino acid motifs that jointly comprise the catalytic site of the RuvC-like nuclease.

Fig. 4.

—Capture of CRISPR-Cas systems and cas genes by mobile genetic elements. The genes are shown by block arrows (not to scale). The CRISPR arrays are shown as in figure 2. The curved arrows show recruitment of CRISPR-Cas systems or individual cas genes by mobile genetic elements.

Fig. 5.

—An alternative hypothetical scenario of the CRISPR-Cas origin: both modules from the same Casposon? The putative ancestral Casposon is a hypothetical construct that does not precisely correspond to any Casposon so far identified. The curved arrows show putative ancestor–descendent relationships. The CRISPR array (depicted as in fig. 2) is tentatively derived from the casposon TIR. The evolution of the effector complex is speculated to have involved an initial duplication of the PALM domain of the Casposon DNA polymerase, in a development of the previously proposed evolutionary scenario (Makarova etal. 2013a). The abbreviations are as in the other figures.