Genomic loci of the Porphyromonas gingivalis insertion element IS1126

The Porphyromonas gingivalis genome contains multiple copies of insertion e lement IS1126. When chromosomal DNA digests of different strains were probe d with IS1126, between 25 and 35 hybridizing fragments per genome were dete cted, depending on the strain, Unrelated strains had very different restric tion fragment length polymorphism (RFLP) patterns. When different laborator y copies of a specific strain were examined, the IS1126 RFLP patterns were very similar but small differences were observed, indicating that element a ssociated changes had occurred during laboratory passage. Within the nest y ear, genome sequencing, assembly, and annotation for P. gingivalis W83 will be completed. Because repetitive elements complicate the assembly of rando mly sequenced DNA fragments, we isolated and sequenced the flanking regions of IS1126 copies in strain W83, We also isolated and sequenced the flankin g regions of IS1126 copies in strain ATCC 33277 in order to compare inserti on sites in phylogenetically divergent strains, We identified 37 new sequen ces flanking IS1126 from strain ATCC 33277 and 30 from strain W83, The inse rtion element was found between genes except where it transposed into anoth er insertion element. Examination of identifiable flanking genes or open re ading frames indicated that the insertion sites were different in the two s trains, except that both strains possess an insertion adjacent to the Lys-g ingipain gene (J. P. Lewis and F. L. Macrina, Infect, Immun, 66:3035-3042, 1998). Most of the genes or sequences flanking IS1126 in ATCC 33277 were pr esent in W83 but were contiguous and not insertion element associated. Thus , where genes were identified in both strains, their order was maintained, indicating that the two genomes are organized similarly, but the loci of IS 1126 are different, In both strains, insertion element-associated duplicate d target sites were lost from several copies of IS1126, providing evidence of homologous recombination between elements. Larger organizational differe nces between the genomes, such as deletions and inversions, may result from insertion element-mediated recombination events.