Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Evolutionary Dynamics of CRISPR-Cassettes in the Metagenome Sorcerer II

CRISPR systems constitute a new type of the prokaryotic anti-phage immunity. It was recently discovered in a half of all known bacteria and almost all known archaea. A typical CRISPR system consists of a set of CRISPR-associated (cas) genes, a CRISPR-cassette, which is a group of short direct repeats separated by short unique spacers. The spacers represent fragments of foreign DNA previously encountered by the host. They allow the host to trigger a specific DNA degradation mechanism if the source DNA invades the cell once again.

There are no effective tools for detection of CRISPR-cassettes applicable for analysis of huge volumes of data, like, e.g., metagenomic samples. Applications of three publicly available programs produce drastically different outputs, clearly overloaded with false positives. To search for CRISPR-cassettes in metagenomes we developed a technique based on a combination of all three programs.

The application of this technique to the Sorcerer II metagenome data produced 192 cassettes with 1908 unique spacers. The identified CRISPR-cassettes were collected in a special database. Families of related cassettes were constructed by the analysis of similarity between repeat units. Additional analysis of flanking regions allowed us to distinguish between the lateral transfer and the parallel evolution of cassettes in related strains. The similarity between related cassettes varied from a single shared spacer up to almost identical cassettes in different genomic locations. For every case we reconstructed the evolutionary history using a limited vocabulary of elementary events.

Both types of similarity hits, those with phage-related spacers and those representing lateral transfers of cassettes, were significantly enriched in metagenome contigs from the same geographical locations. This shows that on-going phage-host encounters in specific ocean locations involves the CRISPR-mediated response and imprints the host genome.


This work is partially supported by the Russian Academy of Sciences (programs ?Molecular and Cellular Biology? and ?Fundamental problems of Oceanology?).

Irena I. Artamonova1,2*
Valery A. Sorokin3
Mikhail S. Gelfand2,3

1Vavilov Inst of General Genetics
RAS, Gubkina 3
119991 Moscow
2Kharkevich Inst for
Information Transmission Problems
RAS, Bolshoi Karetny pereulok 19
127994 Moscow, Russia
3Lomonosov Moscow State Univ
Faculty of Bioengineering and Bioinformatics
Vorobyevy Gory 1-73, Moscow

*Phone: +7(916)9155809