CRISPR-Cas Immunity against Phages: Its Effects on the Evolution and Survival of Bacterial Pathogens

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPR) loci are arrays of short repeats separated by equally short “spacer” sequences [1]–[3]. Along with the CRISPR-associated (cas) genes, they encode an adaptive immune system of archaea and bacteria that protects the cell against viral infection [4]. Remarkably, this system is capable of inserting a short piece of an infecting viral genome as a spacer in the CRISPR array [4], [5] (Figure 1A). The spacer sequence is transcribed and processed to generate a small antisense RNA (the CRISPR RNA or crRNA) (Figure 1B) [6] that is used as a guide for the recognition and destruction of the invader in subsequent infections (Figure 1C) [7]. Thus, spacer acquisition immunizes the bacterium and its progeny against the virus from which it was taken. Because spacers are incorporated in sequential order, CRISPR loci reflect the history of viral infection of the host. Cas proteins participate in all the different steps of this pathway, namely the insertion of spacer sequences into the CRISPR array [8], [9], the biogenesis of crRNAs [10], [11], and the destruction of the infecting viral genome [12], [13]. Figure 1 The CRISPR immunity pathway. Distribution of CRISPR-Cas Loci among Bacterial Pathogens In spite of the unique role that CRISPR-Cas loci play in antiviral defense, they are not universal. To date, the CRISPR database [14], a webtool that determines the presence of CRISPR arrays in completed genomes, indicates that 119/141 archaeal (84%) and 1012/2113 bacterial (48%) genomes contain CRISPR loci. In bacteria, there are species in which all strains have CRISPR loci, some in which only some strains have these loci, and species without strains having CRISPR loci. Therefore it is not possible to determine unequivocally that lack of CRISPR in certain strains or species is due to loss of these loci. However, because CRISPR sequences are spread thorough horizontal gene transfer [15], [16] and can be easily lost [17]–[20], it has been hypothesized recently that CRISPR are in a constant state of flux and can appear and disappear depending on the selective forces of the environment [20]. The same type of uneven distribution is found when we look at the presence of CRISPR loci in bacterial pathogens in the CRISPR database (http://crispr.u-psud.fr/crispr/).