Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome

Abstract

Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocean Sampling expedition. The application of three publicly available CRISPR recognition programs to the Global Ocean metagenome produced a large proportion of false-positive results. To address this problem, a filtering procedure was designed. It resulted in about 200 reliable CRISPR cassettes, which were then studied in detail. The repeat consensuses were clustered into several stable classes that differed from the existing classification. Short fragments of DNA similar to the cassette spacers were more frequently present in the same geographical location than in other locations (P, <0.0001). We developed a catalogue of elementary CRISPR-forming events and reconstructed the likely evolutionary history of cassettes that had common spacers. Metagenomic collections allow for relatively unbiased analysis of phage-host interactions and CRISPR evolution. The results of this study demonstrate that CRISPR cassettes retain the memory of the local virus population at a particular ocean location. CRISPR evolution may be described using a limited vocabulary of elementary events that have a natural biological interpretation.

FIG. 1.

Venn diagram of the numbers of CRISPR cassettes identified by the three programs.

FIG. 2.

Schematic representation of the data flow in the procedure developed for the identification of reliable CRISPR cassettes in metagenomic data. The number of CRISPR cassettes identified by each procedure is given. The number of cassettes added to the set of reliable cassettes at each step is shown in parentheses.

FIG. 3.

Evolutionary events forming CRISPR cassettes. Shown are classes of evolutionary events observed in reliable cassettes and examples of complex relationships. b, rectangles represent cassette spacers; highly similar spacers are indicated by coinciding tones and linked by thin lines. c, spacers are numbered separately in each cassette.