Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis

Abstract

The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MITEPgRS (MITE of P. gingivalis with Repeating Sequences).

Post-translational regulation of a Porphyromonas gingivalis regulator

“…By protein BLAST (Basic Local Alignment Search Tool, https://blast.ncbi.nlm.nih.gov/) PGN_1185 has 98–100% amino acid identity to a GNAT acetyltransferase in 13 P. gingivalis strains with genome sequences deposited in GenBank [32]. According to HOMD (Human Oral Microbiome Database, http://www.homd.org/), there are 10 acetyltransferases in the ATCC 33277 genome [32].…”

“…By protein BLAST (Basic Local Alignment Search Tool, https://blast.ncbi.nlm.nih.gov/) PGN_1185 has 98–100% amino acid identity to a GNAT acetyltransferase in 13 P. gingivalis strains with genome sequences deposited in GenBank [32]. According to HOMD (Human Oral Microbiome Database, http://www.homd.org/), there are 10 acetyltransferases in the ATCC 33277 genome [32]. Of these, six were annotated as follows: a probable serine acetyltransferase (PGN_0230); a metal binding acetyltransferase (PGN_0913); an alginate O-acetyltransferase (PGN_0943); a lipid phospholipid acetyltransferase (PGN_1142); a probable 1-acyl-sn-glycerol 3-phosphate acetyltransferase (PGN_1384); and a lysophospholipid acetyltransferase (PGN_2086).…”

“…The remaining three (PGN_0932, PGN_1389, PGN_1729) were annotated as GNAT acetyltransferases, and the present study confirms that PGN_1185 is a fourth. A possible fifth is the VimA multifunctional protein (PGN_1056 in ATCC 33277) annotated as virulence modulating gene A [32] and subsequently as an acetyltransferase [26]. The conserved domain of VimA places it in the NAT_SF super family which includes GNAT as well as other enzymes.…”

Two-component signal transduction systems in oral bacteria

“…A mutant in the PGN_0752 HK ( haeS ) from ATCC 33277 could not be generated using DNA primers designed from the W83 genome sequence, and in a previous study it was noted that the genomic region surrounding this TCS was highly divergent between the strains [52]. Following publication of the genome sequence of ATCC 33277 [53], a comparison of these regions revealed a 2.529 kbp deletion in ATCC 33277 at the locus homologous to haeSR (PG0719-720) in W83. Thus, ATCC 33277 is a naturally occurring mutant in the TCS.…”

Genetic exchange and reassignment in Porphyromonas gingivalis

“…It was concluded that P. gingivalis uses domain rearrangements and genetic exchange to generate diversity in specific surface virulence factors. When the whole-genome sequences between ATCC 33277 and W83 were determined, extensive rearrangements were found between the two strains, possibly induced by different mobile elements (insertion sequences, miniature inverted-repeat transposable elements, and conjugative transposons) [10]. In ATCC 33277, many of the genes showed higher similarity to the genes of other bacterial species such as Bacteroides fragilis than to genes in W83.…”