Evolutionary plasticity and functional versatility of CRISPR systems

Abstract

The principal biological function of bacterial and archaeal CRISPR systems is RNA-guided adaptive immunity against viruses and other mobile genetic elements (MGEs). These systems show remarkable evolutionary plasticity and functional versatility at multiple levels, including both the defense mechanisms that lead to direct, specific elimination of the target DNA or RNA and those that cause programmed cell death (PCD) or induction of dormancy. This flexibility is also evident in the recruitment of CRISPR systems for nondefense functions. Defective CRISPR systems or individual CRISPR components have been recruited by transposons for RNA-guided transposition, by plasmids for interplasmid competition, and by viruses for antidefense and interviral conflicts. Additionally, multiple highly derived CRISPR variants of yet unknown functions have been discovered. A major route of innovation in CRISPR evolution is the repurposing of diverged repeat variants encoded outside CRISPR arrays for various structural and regulatory functions. The evolutionary plasticity and functional versatility of CRISPR systems are striking manifestations of the ubiquitous interplay between defense and "normal" cellular functions.

Fig 1. Organizational and functional diversity of CRISPR as adaptive immune systems.

General organization of loci encoding different CRISPR-Cas systems is shown. The protein-coding genes are denoted by arrows (not to scale). Homologous genes are shown by the same color. The arrows with dashed outline identify genes that are optional in the respective loci. Adaptation module genes are semitransparent. Gene names are indicated according to the established nomenclature [11]. Vertical arrows indicate genes that are directly involved in target cleavage or cOA synthesis. Anc, ancillary gene; CARF, CRISPR-associated Rossmann fold; Eff, effector domain; PALM, PALM domain involved in cOA synthesis; RuvC-like, HNH, HEPN, HD, PD-DExK, PIN, RelE, nucleases of the respective families.

Fig 2. Exaptation of derived CRISPR systems for functions distinct from adaptive immunity.

Designations of protein-coding genes and cas gene names are the same as in Fig 1. The thin arrows pointing from the schematics in the left part of the figure to those in the right part indicate the inferred directionality of evolution, from stand-alone CRISPR systems to derived ones associated with transposons or STAND NTPases. Left (L) and right (R) ends of the IS elements are shown as brown rectangles, respectively and are not to scale. The terminal integration site (TG) is shown by a small dark gray arrow. The gray arrow generically denotes transposon cargo genes. The Tn7 transposon genes (tnsA, B, C, and tniQ) are designated according to the established classification [69]. DEDD, nuclease of the respective family; other abbreviations are the same as in Fig 1.

Fig 3. Origins and evolution of CRISPR-Cas systems: Initial accretion of components and subsequent reduction.

The figure schematically shows the hypothetical evolutionary scenarios for the common varieties of CRISPR systems and their derivatives. Genes are shown by block arrows not drawn to scale. Protein and domain families are denoted by color. The evolutionary events thought to have been involved in each step are briefly described to the right of the schematics. Inverted repeats flanking transposable elements (IscB and InpB) are shown by triangles. The multipronged arrows pointing to type V indicate the origin of the effector genes of different subtypes from different families of TnpB as well as independent origins of the adaptation modules. The 3 distinct sequence motifs that comprise the catalytic site of the RuvC-like nucleases in IscB, Cas9, TnpB, and Cas12 are denoted I, II, and III.

Fig 4. Exaptation of CRISPR repeats for regulatory functions.

Schematic representation of the functions of repurposed CRISPR repeats. Designations are the same as in Fig 1.