It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements

Abstract

Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.

Keywords: CRISPR-Cas; bacteria; evolution; phage.

Fig. 1.

Lytic phage-mediated selection for CRISPR-Cas–mediated immunity and envelope resistance. Invasion conditions. (A) Monte Carlo simulations of selection for CRISPR-Cas immunity and resistance in a CRISPR⁺ phage-sensitive population initially at equilibrium with the phage. Mean and SE of the changes in density of CRISPR⁺ immune and resistant bacteria across 100 runs. Green bars are for a population of CRISPR⁺ bacteria that cannot generate resistant mutants. Red and blue bars are for populations that can evolve both CRISPR-Cas immunity (red bars) and envelope resistance (blue bars) with equal probabilities. (B) Invasion of CRISPR⁺ into a population of CRISPR⁻-sensitive bacteria at equilibrium with phage, with different initial frequencies of CRISPR⁺ (blue = 0.1, orange = 0.01, green = 0.001, red = 0.0001). Resistant and immune bacteria can be generated in the invading CRISPR⁺ population, and resistance can be generated in the initially dominant CRISPR⁻ population. Mean and SE of the frequency of CRISPR⁺ bacteria over time across 200 runs. Parameters: v_C = v_CI = v_CR = 0.7, δ = 10⁻⁷, β = 50, e = 5 × 10⁻⁷, k = 1, RR = 500, w = 0.1, r(0) = 500, µ_SR = 10⁻⁸, µ_RS = 10⁻⁸, x = 1.667 × 10⁻⁸, and the total volume of the vessel is Vol = 100 mL The initial densities of bacteria and phage in these simulations are at the equilibrium for a phage-limited population: C* = 2 × 10⁴ and V* = 6 × 10⁶, respectively.

Fig. 2.

Selection mediated by temperate phage. (A) The establishment of CRISPR immunity in a population of CRISPR⁺ bacteria at equilibrium with a temperate phage. Changes in the density of CRISPR-Cas immune bacteria are depicted [colony forming units per milliliter (cfu*ml⁻¹)]. (B) The invasion of CRISPR⁺ bacteria into a population of CRISPR⁻ bacteria at equilibrium with a temperate phage. Changes in the densities of CRISPR⁺ bacteria are depicted. Carrying the prophage is associated with a 14% advantage, a 10% cost, a 25% cost, or no cost, as indicated. The parameter values are SI Appendix, Fig. S5 C and F.