CRISPR/Cas System and Resistance to Bacteriophage Infection

Abstract

Bacteria and phages co‐evolve in their environments through an arm‐race with bacteria developing strategies to combat infection by diverse phages, while phages finding ways to circumvent them. Clustered regularly interspaced short palindromic repeats (CRISPR) loci, along with several Cas (CRISPR‐associated) proteins, represents a form of immune system widespread in Bacteria and Archaea. The CRISPR loci evolve through the incorporation of short deoxyribonucleic acid (DNA) sequences (spacers), derived mostly from extrachromosomal DNA such as phage or plasmid sequences, between two partially palindromic repeats. A CRISPR transcript is produced and cleaved within the repeats by Cas protein(s) with or without other host proteins to produce smaller ribonucleic acid fragments (RNAs). These small mature RNAs and Cas proteins target and cleave through base complementarity the invading nucleic acids to ensure cell defence. Phages can also evade the CRISPR/Cas system through point mutations or deletions, forcing the host to adapt by either acquiring new spacers or relying on other defence systems. Hence, phage/host interactions can be appreciated at a microbial population‐wide level through the dynamism of CRISPR/Cas loci.

Key Concepts:

  • CRISPR/Cas loci are composed of multiple repeat‐spacer units associated with a group of specific genes (cas genes).

  • The spacers (short DNA sequences mainly from extrachromosomal elements including foreign DNA) are inserted into CRISPR loci and serve as a molecular directory and memory to prevent future invasion.

  • CRISPR/Cas system prevents bacteriophage infection and plasmid transfer.

  • Depending on the CRISPR/Cas system, the DNA (or RNA) target is cleaved within the proto‐spacer (homologous spacer sequence in the invading element).

  • The successful cleavage of the target relies on the identity between the bacterial spacer and the target (proto‐spacer).

  • CRISPR loci are highly variable and constantly respond to a phage/host or plasmid/host co‐evolution.

  • The CRISPR/Cas can inadvertently acquire self‐DNA and be responsible for some form of auto‐immunity, presumably leading to cell death. To survive this self‐attack, either the targeted genomic DNA is altered by mutation/deletion or the CRISPR/Cas locus is inactivated.

  • By preventing introduction of plasmid, the CRISPR/Cas system can be used to limit the spread of antibiotic resistance genes.

  • Natural bacteriophage insensitive mutants or plasmid interfering mutants can be generated to respectively increase the efficiency or the safety of industrial strains.

Keywords: CRISPR; bacteriophage; plasmid; bacterial immunity; antibiotic resistance; bacterial autoimmunity

Figure 1.

General CRISPR locus model. The arrow in the leader indicates the promoter whereas the arrows in the repeat loop indicate the putative cleavage site (when putative stem‐loop structures are predicted).

Figure 2.

Examples of different CRISPR/Cas loci organisations. Grey arrows indicate core Cas proteins whereas white arrows indicate other Cas proteins. Hatched arrows show additional proteins. CRISPR loci are indicated by black diamonds and coloured boxes series. L, Leader sequence; T, terminal repeat. Figure adapted from Barrangou et al., Brouns et al. and Haft et al..

Figure 3.

Adaptation and interference stages of the CRISPR/Cas system. (a) Stage I: Adaptation. When DNA enters the cell through infection, transformation, conjugation, or transduction, new DNA spacers can be acquired and are generally integrated at the 5′‐end of the CRISPR locus. The mechanism and protein(s) involved in the spacer acquisition are unknown. If no spacer is acquired, the phage lytic cycle or plasmid replication can proceed (not shown). (b) Stage II: Interference. The CRISPR locus is transcribed and processed in small crRNAs. Cas complexes bind to crRNAs and are guided to foreign DNA matching the crRNA sequence. This recognition is followed by a specific cleavage within the proto‐spacer. Self‐DNA can also be targeted by the CRISPR/Cas system leading to autoimmunity. If there is no adequate pairing between the spacer and the proto‐spacer (as in the case of a phage mutant), replication of the invasive genetic material can occur. Figure inspired by Deveau et al.. crRNA, CRISPR RNA; PAM, proto‐spacer adjacent motif.

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Garneau, Josiane E, and Moineau, Sylvain(Jul 2011) CRISPR/Cas System and Resistance to Bacteriophage Infection. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0023273]