Evolutionary Dynamics of Clustered Irregularly Interspaced Short Palindromic Repeat Systems in the Ocean Metagenome
- 1 April 2010
- journal article
- research article
- Published by American Society for Microbiology in Applied and Environmental Microbiology
- Vol. 76 (7), 2136-2144
- https://doi.org/10.1128/aem.01985-09
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.Keywords
This publication has 43 references indexed in Scilit:
- New dimensions of the virus world discovered through metagenomicsTrends in Microbiology, 2010
- Viral biogeography revealed by signatures in Sulfolobus islandicus genomesEnvironmental Microbiology, 2009
- CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNAScience, 2008
- Small CRISPR RNAs Guide Antiviral Defense in ProkaryotesScience, 2008
- Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial CommunitiesScience, 2008
- Phage Response to CRISPR-Encoded Resistance in Streptococcus thermophilusJournal of Bacteriology, 2008
- Population Dynamics and Diversity of Viruses, Bacteria and Phytoplankton in a Shallow Eutrophic LakeMicrobial Ecology, 2007
- CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeatsNucleic Acids Research, 2007
- The Repetitive DNA Elements Called CRISPRs and Their Associated Genes: Evidence of Horizontal Transfer Among ProkaryotesJournal of Molecular Evolution, 2006
- MUSCLE: multiple sequence alignment with high accuracy and high throughputNucleic Acids Research, 2004