Analysis of a genomic island housing genes for DNA S-modification system in Streptomyces lividans 66 and its counterparts in other distantly related bacteria

The complete sequence (92,770-bp) of a genomic island (GI) named SLG from Streptomyces lividans 66, encoding a novel DNA S-modification system (dnd), was determined. Its overall G+C content was 67.8%, lower than those of three sequenced Streptomyces genomes. Among eighty-five predicted open reading frames (ORFs) in SLG, twenty-two ORFs showed little homology with previously known proteins. SLG displays a mosaic structure composed of four modules, indicative of multiple recombination events in its formation. Spontaneous excision and circularization of SLG was observed, and the excision rate appeared to be induced at least five-fold by MNNG exposure. Using constructed mini-islands of SLG, we demonstrated that Slg01, a P4-like integrase, was sufficient to promote SLG integration, excision and circularization. Eleven counterpart dnd clusters, which also mapped to GIs in ten chromosomes and a plasmid, were found in taxonomically unrelated bacterial species from various geographic niches. Additionally, ca. 10% of actinomycetes were found to possess a dnd cluster in a survey involving 74 strains. Comparison of dnd clusters in the twelve bacteria strongly suggests that these dnd-bearing elements might have evolved from a common ancestor similar to plasmid-originated chromosome II of Pseudoalteromonas haloplanktis TAC125.