Genetic exchange and reassignment in Porphyromonas gingivalis

Abstract

Porphyromonas gingivalis is considered a keystone pathogen in adult periodontitis but has also been associated with systemic diseases. It has a myriad of virulence factors that differ between strains. Genetic exchange and intracellular genome rearrangements may be responsible for the variability in the virulence of P. gingivalis. The present review discusses how the exchange of alleles can convert this bacterium from commensalistic to pathogenic and potentially shapes the host-microbe environment from homeostasis to dysbiosis. It is likely that genotypes of P. gingivalis with increased pathogenic adaptations may spread in the human population with features acquired from a common pool of alleles. The exact molecular mechanisms that trigger this exchange are so far unknown but they may be elicited by environmental pressure.

Keywords: Porphyromonas gingivalis; adaptability; dysbiosis; homeostasis; keystone pathogen hypothesis; periodontitis; survival.

Figure 1.

Major and minor fimbrilin proteins encoded in the 35 P. gingivalis genomic sequences. All the fimbrilin proteins were detected in the following manner: The keyword FimA/Mfa1/fimbrilin were used to select from the proteins predicted in the 35 genomes, which were annotated by the NCBI prokaryotic genome annotation pipeline [54]. The keywords were also used to search for P. gingivalis FimA from the NCBI protein databases. These “seed” proteins were then searched against all the proteins in the 35 genomes to identify additional fimbrilin candidates. These potential candidates matched with the seed proteins at ≥ 90% sequence identity and ≥ 90% length coverage. The additional candidates were combined with other annotated fimbrilin proteins and aligned with the “mafftℍ program [55]. The aligned sequences were used to build a phylogenetic tree with the “FastTree” program [56]. For each fimbrilin shown in the tree, the Genbank accession number was printed first, followed with the strain label (in blue), the original functional annotation (by NCBI), and the size of the protein sequences in amino acids (red).

Figure 2.

Syntenic analysis of 9 P. gingivalis genomic sequences. Of the 35 currently available P. gingivalis genomics sequences, eight are considered finished with one final successfully assembled contig. The sequence of JCVI SC001 appears to have a one-contig circular sequence under the Genbank Accession number CM001843, however it is a pseudo-contig generated by ordering the 284 unassembled contigs using the sequence of strain TDC60 as the template. Thus, the syntenies, illustrated as the same color across different genomes, of JCVI SC001 appear to be in similar order of those in TDC60 and may not be the true order in this genome. Syntenies were detected with the “MUAVE” program (version 2.4.0) [57] and were illustrated as rectangles of the same colors across all genomes. Two groups of syntenies were indicated with blue and red arrows underneath to exemplify the different rearrangement and inversion events in different genomes for this species.