In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

Abstract

Currently, genome sequences of a total of 19 Porphyromonas gingivalis strains are available, including eight completed genomes (strains W83, ATCC 33277, TDC60, HG66, A7436, AJW4, 381, and A7A1-28) and 11 high-coverage draft sequences (JCVI SC001, F0185, F0566, F0568, F0569, F0570, SJD2, W4087, W50, Ando, and MP4-504) that are assembled into fewer than 300 contigs. The objective was to compare these genomes at both nucleotide and protein sequence levels in order to understand their phylogenetic and functional relatedness. Four copies of 16S rRNA gene sequences were identified in each of the eight complete genomes and one in the other 11 unfinished genomes. These 43 16S rRNA sequences represent only 24 unique sequences and the derived phylogenetic tree suggests a possible evolutionary history for these strains. Phylogenomic comparison based on shared proteins and whole genome nucleotide sequences consistently showed two groups with closely related members: one consisted of ATCC 33277, 381, and HG66, another of W83, W50, and A7436. At least 1,037 core/shared proteins were identified in the 19 P. gingivalis genomes based on the most stringent detecting parameters. Comparative functional genomics based on genome-wide comparisons between NCBI and RAST annotations, as well as additional approaches, revealed functions that are unique or missing in individual P. gingivalis strains, or species-specific in all P. gingivalis strains, when compared to a neighboring species P. asaccharolytica. All the comparative results of this study are available online for download at ftp://www.homd.org/publication_data/20160425/.

Two-component signal transduction systems in oral bacteria

“…As reported above, strain-specific mutations occurring in both FimRS and HaeSR render them non-functional or impaired. Therefore, studies comparing multiple strains such as that recently reported by [79] provide a valuable resource to discover more strain-specific differences that could impact infection.…”

Genetic exchange and reassignment in Porphyromonas gingivalis

“…Probably exchange of DNA in biofilms by transformation is important to the ecology and persistence of P. gingivalis in the challenging environment of the periodontal pocket and to evasion of host immune defences and immunization strategies [6,9]. P. gingivalis appears to have both a core genome [7,11] and a flexible, dispensable genome. Sampling of DNA from the flexible genome could imply adaptation for the bacterium to the changing environment [7], which is supported by the genetic diversity of P. gingivalis.…”

“…At least 95% of clinical strains from P. gingivalis harbours CRISPR arrays [41]. The presence of transposases and CRISPR-associated sequences in P. gingivalis [11] suggested that some parts of the P. gingivalis genome are mobile so that rearrangement or horizontal gene transfer from one strain to another can take place [20]. In the P. gingivalis W83 genome, all four CRISPR regions were transcribed and one of them was active against dsDNA in vivo [41].…”

“…Phylogenomic comparison based on shared proteins and whole-genome nucleotide sequences consistently showed two groups among 19 P. gingivalis strains examined with closely related members: one consisted of ATCC 33277, 381 and HG66, the other of W83, W50 and A7436 [11]. Among them, ATCC 33277 and W83 were mono-clonal but fell in different groups.…”

“…Obviously, other factors than just clonality affect the virulence of P. gingivalis strains. Comparative functional genetics showed strain difference in gingipains, attachment, heme, gene mobility, transposases, capsules, CRISPR and phage [11]. …”