We examined the five genomes of G. vaginalis available in the NCBI genome database that had spacers targeting coding and non-coding regions on the ABT-263 in vivo chromosomes of strains 409–05, 6420B, 315A, 41 V, ATCC14019,

and AMD. We did not find a match between the spacers and the endogenous genomic sequences, except for the sequences located in the CRISPR arrays. We also analysed whether the protospacers located on the G. vaginalis chromosome displayed conserved protospacer adjacent motif (PAM) sequences [41, 42]. We aligned the protospacers with the flanking regions comprising 20 bp on both sides. Alignments were performed for ten JPH203 protospacers sharing 100% identity with the spacers. The conserved motif of two nucleotides (AA) situated immediately upstream of the target region was detected (Figure 5). The PAM signature AA was confirmed for nine protospacers with up to 10% mismatches located distant from the 5′- and 3′-ends of the spacers. Figure 5 WebLogo for the PAM consensus sequence determination. Ten protospacers identical to

spacers were aligned relative to the 5′-end of the protospacer (base 1). Sequences include the protospacer (positive numbers) and 13 nucleotides (negative numbers) upstream of the first base of the protospacer (containing the PAM). Thus, the motifs adjacent to the protospacers located in the G. vaginalis genomic DNA bear the signatures of PAMs. The BIRB 796 datasheet orientation of the G. vaginalis PAM is 5′-AA-protospacer-3′, which coincides with the orientation of the PAM identified in E. coli as CRISPR/Cas; both bacteria belong to the same type [41, 42]. Among all of the G. vaginalis CRISPR unless arrays, the first nucleotide of 97.5% of the spacers was either C or T. Only six spacers started with A or G (2.5%). All of the spacers targeting the protospacers on the G. vaginalis chromosome started with C or T (18:13). Discussion The CRISPR locus of the recently

discovered CRISPR/Cas defence system in prokaryotes protects against invading viruses and plasmids and is a map of the “immunological memory” of the microorganism [25, 26]. The spacer sequences that are incorporated into the CRISPR loci provide a historical view on the exposure of the bacteria to a variety of foreign genetic elements [23]. A recent report on the ability of CRISPR/Cas to prevent natural transformation in Streptococcus pneumoniae enlarged the role of CRISPR in bacterial nucleic acid-based immunity and the impact that CRISPR has on the emergence of bacterial pathogens [43]. In the current study, we analysed the CRISPR arrays in 17 recently characterised G. vaginalis clinical isolates [18] and the genomes of 21 of G. vaginalis strains deposited in the NCBI genome database. We examined the spacer repertoire and evaluated the potential impact of CRISPR/Cas on gene uptake in G. vaginalis. We found that six clinical isolates (35%) and 14 G. vaginalis genomes deposited in the NCBI database (67%) contained CRISPR/Cas loci.