BI82CH09-Wiedenheft ARI 15 May 2013 4:39 CRISPR-Mediated Adaptive Immune Systems in Bacteria and Archaea Rotem Sorek,1 C. Martin Lawrence,2,3 and Blake Wiedenheft4 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel; email: [email protected] 2Thermal Biology Institute, 3Department of Chemistry and Biochemistry, and 4Department of Immunology and Infectious Diseases, Montana State University, Bozeman, Montana 59717; email: [email protected], [email protected] Annu. Rev. Biochem. 2013. 82:237–66 Keywords First published online as a Review in Advance on bacterial immunity, bacteriophage, crRNA, RNA interference, small March 11, 2013 RNAs The Annual Review of Biochemistry is online at biochem.annualreviews.org Abstract This article’s doi: Effective clearance of an infection requires that the immune system 10.1146/annurev-biochem-072911-172315 rapidly detects and neutralizes invading parasites while strictly avoid- Annu. Rev. Biochem. 2013.82:237-266. Downloaded from www.annualreviews.org Copyright c 2013 by Annual Reviews. ing self-antigens that would result in autoimmunity. The cellular ma- Access provided by Weizmann Institute of Science on 08/03/15. For personal use only. All rights reserved chinery and complex signaling pathways that coordinate an effective immune response have generally been considered properties of the eu- karyotic immune system. However, a surprisingly sophisticated adap- tive immune system that relies on small RNAs for sequence-specific targeting of foreign nucleic acids was recently discovered in bacteria and archaea. Molecular vaccination in prokaryotes is achieved by inte- grating short fragments of foreign nucleic acids into a repetitive locus in the host chromosome known as a CRISPR (clustered regularly in- terspaced short palindromic repeat). Here we review the mechanisms of CRISPR-mediated immunity and discuss the ecological and evolu- tionary implications of these adaptive defense systems. 237 BI82CH09-Wiedenheft ARI 15 May 2013 4:39 environmental and medical science is currently Contents reaching a new crescendo. In the 1980s, marine virologists reported that one liter of sea water INTRODUCTION.................. 238 contains approximately ten billion bacterio- CRISPR DESIGN AND phages, and today these viruses are generally DISTRIBUTION................. 238 considered the most abundant and diverse CRISPRs AND THEIR biological entities on Earth (2–4). The selective ASSOCIATED PROTEIN pressures imposed by these viral predators have MACHINERY.................... 239 a profound impact on the composition and the Type I CRISPR-Associated behavior of microbial communities in every Systems........................ 241 ecological setting (5), and microbial hosts have Type II CRISPR-Associated evolved various mechanisms to evade infec- Systems........................ 243 tion (6–9). Historically our appreciation for Type III CRISPR-Associated microbial immune systems had been restricted Systems........................ 244 to innate defense mechanisms (e.g., restriction IMMUNE SYSTEM ACTIVATION modification and receptor switching), but a ANDREGULATION............. 244 nucleic acid–based adaptive immune system THREE STAGES OF was recently discovered (10–13). Bacteria and CRISPR-MEDIATED archaea acquire resistance to viral and plasmid IMMUNITY...................... 245 challengers by integrating short fragments of CRISPRAdaptation............... 245 foreign nucleic acid into the host chromosome CRISPR RNA Biogenesis . 249 at one end of a repetitive element known as Finding Your Foe: Target a CRISPR (clustered regularly interspaced Surveillance and Destruction . 253 short palindromic repeat). CRISPR-mediated ECOLOGICAL IMPLICATIONS adaptive immunity proceeds in three distinct OF ADAPTIVE IMMUNITY . 255 stages: acquisition of foreign DNA, CRISPR Sampling of CRISPRs in Microbial RNA (crRNA) biogenesis, and target interfer- Communities................... 256 ence (Figure 1a). Although these three basic MathematicalModeling............ 256 stages appear to be common to all CRISPR The Influence of CRISPR systems, CRISPR loci and the proteins that onPhageDiversity.............. 257 mediate each stage of adaptive immunity The Role of Horizontal Gene are remarkably diverse (Figure 1b). Here Transfer in CRISPR-Phage we review the functional diversity among Interactions..................... 258 different versions of this immune system and discuss the evolutionary implications of this Annu. Rev. Biochem. 2013.82:237-266. Downloaded from www.annualreviews.org rapidly evolving, heritable immune system on Access provided by Weizmann Institute of Science on 08/03/15. For personal use only. microbial evolution. INTRODUCTION In the late 1800s, Ernest Hanbury Hankin (1) reported that water from the Ganges and CRISPR DESIGN AND Yamuna rivers in India contained an antibac- DISTRIBUTION terial agent that killed Vibrio cholerae.These CRISPRs are a diverse family of DNA re- filterable agents, later termed bacteriophages peats that all share a common architecture. (from “bacteria” and the Greek word phagein, Each CRISPR locus consists of a series of “to devour”), were heralded as a potential treat- short repeat sequences [typically 20–50 base ment for diseases. Although phages have yet pairs (bp) long] separated by unique spacer to reach their therapeutic potential in clinical sequences of a similar length (Figure 1a). The settings, the importance of bacteriophages in repeat sequences within a CRISPR locus are 238 Sorek · Lawrence · Wiedenheft BI82CH09-Wiedenheft ARI 15 May 2013 4:39 conserved, but repeats in different CRISPR this skewed distribution remains speculative, loci can vary in both sequence and length an assessment of 24 Enterococcus faecalis genome (14). Phylogenetic analyses of CRISPR repeat sequences revealed an inverse correlation sequences have shown that CRISPRs can be between the presence of a CRISPR/Cas locus organized into clusters based on the sequence and antibiotic resistance (20). similarity of their repeat sequences. Some An adenine and thymine (AT)-rich sequence repeats are palindromic and are predicted to called a leader often flanks CRISPR loci. Com- generate RNAs with stable hairpin structures, parative analyses have shown that spacer se- whereas others are predicted to be unstructured quences nearest the leader are most diverse, (Figure 1b) (14). Despite the extreme diversity whereas repeats farthest from the leader (in the of CRISPR repeat sequences, most repeats region known as the trailer) are often degener- have a conserved GAAA(C/G) motif at the 3 ate (21, 22). Although the function of CRISPRs end, which may serve as a binding site for one was unknown at the time of this initial obser- or more of the conserved Cas proteins (14–16). vation, the leader-end diversity and trailer-end In addition to repeat and spacer sequence degeneracy indicated these loci had polarity de- diversity, the number of CRISPR loci and the fined by the position of the leader. We now length of each locus are also variable. It is not know that the leader sequences contain pro- uncommon for a single prokaryotic chromo- moter elements (23–26) and binding sites for some to contain multiple CRISPR loci (e.g., 18 regulatory proteins (25, 26) critical to crRNA CRISPR loci in Methanocaldococcus sp. FS406- expression and new sequence acquisition (27). 22), and some of these loci can be thousands of base pairs in length (hundreds of repeat- CRISPRs AND THEIR spacer units). The number of distinct CRISPR ASSOCIATED PROTEIN loci and the length of these repetitive arrays MACHINERY do not correlate with genome size; some of In addition to the leader sequence, comparative the smallest microbial genomes (e.g., Nanoar- analyses have also identified a variable cassette chaeum equitans) contain multiple CRISPR loci, of cas genes, which is typically located adjacent and CRISPRs in some genomes account for to a CRISPR locus (Figure 1b). Four cas genes more than 1% of the chromosome (e.g., Sul- were initially identified in genomes contain- folobus solfataricus). ing CRISPRs (21), but accumulating genome The repeat-spacer-repeat pattern now sequences and the implementation of increas- considered to be the defining characteristic ingly sophisticated search methods have led to of a CRISPR locus was initially described the identification of ∼45 different gene families in Escherichia coli in 1987 (17). However, the commonly found in association with CRISPRs prevalence and phylogenetic distribution of (28). Six of these cas genes (cas1–cas6) are widely Annu. Rev. Biochem. 2013.82:237-266. Downloaded from www.annualreviews.org these repetitive elements were not appreciated conserved and are considered core cas genes, Access provided by Weizmann Institute of Science on 08/03/15. For personal use only. for more than a decade (16). Computational but only cas1 and cas2 are universally conserved methods for detecting these repeat patterns in genomes that contain CRISPR loci (28, 29). have been developed, and there are cur- cas1 is a hallmark of this immune system, and rently two web-based utilities (CRISPRdb phylogenetic analysis of cas1 sequences suggests and CRISPI) dedicated to the identification several distinct versions of CRISPR systems ex- and annotation of CRISPRs and CRISPR- ist (28, 29). Each of these different phylotypes is associated (cas) genes (18, 19). Interestingly, defined by a unique composition and conserved CRISPRs are unevenly distributed between arrangement of cas genes. Remarkably,