Abstract
BackgroundCRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.ResultsTo this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.ConclusionsThe observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-663) contains supplementary material, which is available to authorized users.
Highlights
Clustered regularly interspaced short palindromic repeats (CRISPR) is a microbial immune system likely to be involved in host-parasite coevolution
We investigate the underrepresentation of Protospacer associated motif (PAM) in bacteriophages that encounter CRISPR systems
Phages infecting all bacteria We analyzed two data sets, one including any suitable data, and one focusing on the Streptococcus genus, where the CRISPR system is particualarly well understood
Summary
CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. Cas genes characteristically show high rates of evolution, both in the protein sequence and in the operon structure resulting in different CRISPR/Cas types [2]. This high diversity has been attributed to host-parasite coevolution [3]. New spacer sequences are acquired from invasive elements that are incorporated into the CRISPR array These sequences are the basis of the sequence-specific immune response. In the interference stage, crRNAs and associated Cas proteins target and bind protospacers (sequences complementary to spacers) leading to cleavage and degradation of the foreign genetic material
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