Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution.

M Senthil Kumar,Sridhar Hannenhalli,Joshua B Plotkin,Eugene V Koonin

doi:10.1371/journal.pcbi.1004603

M Senthil Kumar, Sridhar Hannenhalli + Show 2 more

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https://doi.org/10.1371/journal.pcbi.1004603

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Abstract

CRISPRs offer adaptive immunity in prokaryotes by acquiring genomic fragments from infecting phage and subsequently exploiting them for phage restriction via an RNAi-like mechanism. Here, we develop and analyze a dynamical model of CRISPR-mediated prokaryote-phage coevolution that incorporates classical CRISPR kinetics along with the recently discovered infection-induced activation and autoimmunity side effects. Our analyses reveal two striking characteristics of the CRISPR defense strategy: that both restriction and abortive infections operate during coevolution with phages, driving phages to much lower densities than possible with restriction alone, and that CRISPR maintenance is determined by a key dimensionless combination of parameters, which upper bounds the activation level of CRISPRs in uninfected populations. We contrast these qualitative observations with experimental data on CRISPR kinetics, which offer insight into the spacer deletion mechanism and the observed low CRISPR prevalence in clinical isolates. More generally, we exploit numerical simulations to delineate four regimes of CRISPR dynamics in terms of its host, kinetic, and regulatory parameters.

Highlights

Prokaryotes have evolved diverse molecular defense systems over billions of years of co-evolution with phages [1,2]
Bacteria and archaea have evolved a variety of defense systems
These can broadly be classified into either restriction or suicide mechanisms. The former enforces nicks in the invading DNA making it unusable for production of further infectious particles; the latter, by contrast, induces cell death whereby an infected cell activates specific host suicidal pathways that are otherwise strongly repressed, inhibiting further infection. Examples of the former class include restriction-modification (R-M) and the recently discovered Clustered Regularly Interspersed Palindromic Repeats (CRISPRs) systems, while the latter class includes a variety of toxin/ anti-toxin systems

Summary

Introduction

Prokaryotes have evolved diverse molecular defense systems over billions of years of co-evolution with phages [1,2]. CRISPR, as a defense mechanism, works via targeted acquisition of 26–72bp fragments (called protospacers) from the target DNA, and subsequently use of acquired fragments (spacers) for target restriction through an RNAi-like mechanism [7,8]. In addition to acquiring phage fragments, CRISPR systems can acquire spacers from the host genome. This has been experimentally demonstrated in two model systems: first, selective induction of the acquisition machinery (in the absence of interference) in laboratory strains of Escherichia coli resulted in the accumulation of a large number of self-targeting spacers [12]; second, abolition of interference activity (and not the acquisition machinery) in wild type Streptococcus thermophilus resulted in unbiased acquisitions of self-targeting spacers alongside phage-targeting spacers [13]. Directed experiments have conclusively shown that self-targeting can result in severe lethality [9,17,18,19,20,21]

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