CRISPR-based adaptive immune systems

Abstract

CRISPR-Cas systems are recently discovered, RNA-based immune systems that control invasions of viruses and plasmids in archaea and bacteria. Prokaryotes with CRISPR-Cas immune systems capture short invader sequences within the CRISPR loci in their genomes, and small RNAs produced from the CRISPR loci (CRISPR (cr)RNAs) guide Cas proteins to recognize and degrade (or otherwise silence) the invading nucleic acids. There are multiple variations of the pathway found among prokaryotes, each mediated by largely distinct components and mechanisms that we are only beginning to delineate. Here we will review our current understanding of the remarkable CRISPR-Cas pathways with particular attention to studies relevant to systems found in the archaea.

Figure 1

Overview of the CRISPR-Cas invader defense pathway. In the adaptation phase, a short fragment of foreign DNA (protospacer) is acquired from the invader and integrated into the host CRISPR locus adjacent to the leader. Protospacer adjacent motifs (PAMs) are found near invader sequences selected for CRISPR integration. The CRISPR locus consists of short direct repeat sequences (black) that separate similarly-sized, invader-derived sequences (multiple colors). In the biogenesis phase of the pathway, CRISPR locus transcripts are processed to release individual mature crRNAs (each targeting a different sequence). Mature crRNAs typically retain some of the repeat sequence, which is thought to provide a recognizable signature of the crRNAs. In the silencing phase, crRNA-Cas protein effector complexes recognize foreign DNA or RNA through basepairing of the crRNA. The Cmr and Csn systems affect cleavage of target RNA and DNA, respectively. PAMs provide important auxiliary signals for the recognition of invaders for some DNA-targeting systems.

Figure 2

Combinations of Cas proteins create diverse CRISPR-Cas systems. Cas1-6 are core Cas proteins found in many and diverse organisms. In addition, there are eight primary modules of subtype-specific Cas proteins (consisting of 2–6 proteins each), and the auxiliary Cmr module. A typical CRISPR-Cas system is comprised of the nearly universal Cas1 and Cas2 proteins, a specific combination of the other core Cas proteins and a set of sub-type specific Cas proteins. A given organism may possess more than one CRISPR-Cas system, and may also have the Cmr module. See Haft et al. [29].

Figure 3

CRISPR-Cas systems of various prokaryotes include three co-evolved components: CRISPR repeats, CRISPR leaders, and associated Cas proteins that function on discrete PAMs (protospacer adjacent elements) present in the viruses and other mobile genetic elements that they encounter. Known and predicted interactions between Cas proteins and the host CRISPR RNA repeat sequences and leader DNA elements plus invader PAMs are indicated (arrows). The specificity of these RNA-protein and DNA-protein interactions likely contribute to the co-evolution of the four components.