Costs of CRISPR-Cas-mediated resistance inStreptococcus thermophilus

Abstract

CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.

Immigration of susceptible hosts triggers the evolution of alternative parasite defence strategies

“…We and others have previously shown that the CRISPR-Cas adaptive immune system of bacteria is associated with an induced cost of resistance [10,13]. This was observed both in P. aeruginosa strain UCBPP-PA14 and in Streptococcus thermophilus strain DGCC7710 [10,13], although in the latter species a constitutive cost of carrying the system was also detected [13].…”

“…We and others have previously shown that the CRISPR-Cas adaptive immune system of bacteria is associated with an induced cost of resistance [10,13]. This was observed both in P. aeruginosa strain UCBPP-PA14 and in Streptococcus thermophilus strain DGCC7710 [10,13], although in the latter species a constitutive cost of carrying the system was also detected [13]. The induced cost of CRISPR may be because of toxic effects from increased Cas protein production, including autoimmunity [36][37][38], or because of phage-induced damage to the host before the phage is destroyed, or both.…”

“…We have previously shown that sm through the loss of the phage receptor is associated with a fixed fitness cost [10][11][12], whereas CRISPR-Cas-mediated defence is associated with an induced fitness cost [10,13]. The induced fitness cost of P. aeruginosa CRISPR-Cas may either be because the system is induced upon infection, as is the case in other species [14 -16], or because of phage-induced damage to the host before it is eliminated.…”

Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system

“…In Streptococcus thermophilus, Cas9 is constitutively produced and it confers a fitness cost that is most pronounced during lag phase and at low cell density, when the risk of phage infection is low (7,13,19). Experiments show that CRISPR-Cas-mediated autoimmunity results in deleterious effects, ranging from genome rearrangements and cell filamentation to suicide (9).…”

“…Expression of CRISPR-Cas adaptive immune systems is costly (7,8), possibly because of autoimmunity (9,10) and deployment of resources that could otherwise be invested in growth. To limit fitness costs, some CRISPR-Cas systems are induced upon infection (11)(12)(13).…”