Restriction Fragment Length Polymorphism Analysis of the Fimbrillin Locus,fimA,of Porphyromonas gingivalis

Abstract

With hybridization probes derived from the fimbrial locus of Porphyromonas gingivalis strain 381, fimA_{381 '} restriction fragment length polymorphisms (RFLPs) were examined at the fimbrillin locus in 39 human and animal strains of this species. The 39 strains were subdivided into nine RFLP groups (I-IX) after genomic digests were probed with the internal coding sequence of the fimA₃₈₁ gene. Thirty-three strains showed one or more AluI fragments of moderate-to-high homology (≥77%) with the internal coding sequence of fimA₃₈₁ . These strains were distributed into the first seven RFLP groups, based solely on the size of the major hybridizing AluI fragment. Five human strains (RFLP Group VIII) had only one Alu I fragment that hybridized very poorly with this probe. One animal strain did not have homology at all (RFLP Group IX). When all AluI fragments that hybridized with fimA₃₈₁ were analyzed, RFLP groups I-VIII were further differentiated into 25 distinct RFLP patterns. Hybridizations were also performed with the internal coding sequence of fimA₃₈₁ to probe PstI genomic digests of selected strains that appeared to have lesser homology with fimA₃₈₁. These hybridizations were performed to determine the level and location of the region of poor homology within the fimA genes of these strains. The results suggested that fimbrial coding sequences are more commonly conserved between these strains in the 5'-region of the fimA locus (≥92% sequence homology). However, the five human strains of RFLP Group VIII had only one PstI fragment that hybridized very poorly with a probe derived from fimA₃₈₁ coding sequence, and this sequence homology (only > 66%) was located in the central or 3'-end of the fimA gene. The 5'-region of the fimA allele in Group VIII strains did not have any detectable sequence homology. In contrast, the Group VIII strains were highly homologous with the sequences flanking the fimA₃₈₁ gene. This indicates that these strains do possess a fimA allele at the same chromosomal location as fimA₃₈₁ .