CRISPR recognizes as many phage types as possible without overwhelming the CAS machinery

Michael W. Deem; PNAS April 7, 2020 117 (14) 7550-7552

In 2007, researchers at Danisco interested in fortifying the lactic acid bacteria used to produce dairy products such as milk and cheese against attack by phage showed that CRISPR provided resistance (1). These phage infections were common in industrial dairy fermentation, and it was hugely significant that insertion of multiple spacers in the bacterial CRISPR system was shown to protect against them. Intriguingly, rare mutations in the phage regions from which these spacers were derived were also shown to give rise to lineages that could again reinfect the bacteria. Thus was born the study of the phage–bacteria immune system arms race. In PNAS, Bradde et al. (2) present a theory of the tradeoff between broad coverage of phage types and efficient use of a limited number of enzymes in each bacterium that leads to an optimal size of the CRISPR immune system.

Earlier bioinformatics studies had shown that the majority of spacers in bacterial CRISPR arrays matched phage or conjugative plasmids that naturally infect the bacteria containing the CRISPR array (3). These CRISPR spacers were found to be the most polymorphic sites in plague Yersinia pestis strains, and thus potentially useful for forensically tracing the origins of prokaryotic pathogens (4). In the same year, bioinformatic analysis showed that spacers from multiple strains and species of Streptococcus were homologous to phage and plasmid sequences (5). The sensitivity of Streptococcus thermophilus to phage was shown to correlate with the number of spacers in the CRISPR locus. A significant number of studies followed up on these observations that bacterial resistance to phage correlated with spacer diversity in the CRISPR array (6⇓–8).

Later studies confirmed the ability of S. thermophilus to insert phage sequences into its CRISPR array and analyzed thousands of spacers from over a hundred strains (9). The data suggested that the activity of CRISPR was correlated with the spacer diversity. Metagenomic studies of Leptospirillum environmental biofilm community species confirmed the extensive diversity of the spacer loci, suggested it was the result of a population-level response to a changing population of phage (6), and emphasized the role of phage evolution in maintaining the diversity of relevant spacers (10).

We now know that CRISPR is an adaptive immune system for bacteria that interacts with the diversity of the phage population (Fig. 1). Due to the insertion of spacers into the leader-proximal position, the CRISPR array provides a record of the phage challenges that the bacteria have faced. However, this record is shaped not only by the prevalence of phage but also by the selective advantages that the different spacers may confer. An early theoretical study showed that in environments with changing phage populations, leader-distal spacers are less diverse than leader-proximal spacers due to the selective pressure for targeting dominant phage genotypes (14), as had been observed in studies of environmental strains. A population dynamics model showed that a less diverse CRISPR spacer distribution that is focused on the most effective spacers evolved when phage had multiple protospacers that differ in their effectiveness, although a diverse spacer locus evolved when phage protospacers differed in their ease of acquisition (15). Moreover, large acquisition probabilities lead to a broader spacer distribution, whereas smaller acquisition probabilities lead to a spacer distribution focused on the most effective spacers. A spatially diverse model showed that the CRISPR array evolved to a length between 20 and 30 spacers (16).

See: https://www.pnas.org/content/117/14/7550

Figure: CRISPR is an adaptive, heritable, genetic immune system for prokaryotes that operates in three phases of adaptation, expression, and interference