PT  - JOURNAL ARTICLE
AU  - Daniel J. Nasko
AU  - Barbra D. Ferrell
AU  - Ryan M. Moore
AU  - Jaysheel D. Bhavsar
AU  - Shawn W. Polson
AU  - K. Eric Wommack
TI  - CRISPR spacers indicate preferential matching of specific virioplankton genes
AID  - 10.1101/487884
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 487884
4099  - http://biorxiv.org/content/early/2018/12/05/487884.short
4100  - http://biorxiv.org/content/early/2018/12/05/487884.full
AB  - Viral infection exerts selection pressure on marine microbes as viral-induced cell lysis causes 20 to 50% of cell mortality resulting in fluxes of biomass into oceanic dissolved organic matter. Archaeal and bacterial populations can defend against viral infection using the CRISPR-Cas system which relies on specific matching between a spacer sequence and a viral gene. If a CRISPR spacer match to any gene within a viral genome is equally effective in preventing lysis, then no viral genes should be preferentially matched by CRISPR spacers. However, if there are differences in effectiveness then certain viral genes may demonstrate a greater frequency of CRISPR spacer matches. Indeed, homology search analyses of bacterioplankton CRISPR spacer sequences against virioplankton sequences revealed preferential matching of replication proteins, nucleic acid binding proteins, and viral structural proteins. Positive selection pressure for effective viral defense is one parsimonious explanation for these observations. CRISPR spacers from virioplankton metagenomes preferentially matched methyltransferase and phage integrase genes within virioplankton sequences. These viriolankton CRISPR spacers may assist infected host cells in defending against competing phage. Analyses also revealed that half of the spacer-matched viral genes were unknown and that some genes matched several spacers and some spacers matched multiple genes, a many-to-many relationship. Thus, CRISPR spacer matching may be an evolutionary algorithm, agnostically identifying those genes under stringent selection pressure for sustaining viral infection and lysis. Investigating this subset of viral genes could reveal those genetic mechanisms essential to viral-host interactions and provide new technologies for optimizing CRISPR defense in beneficial microbes.