Comparative Whole-Genome Analysis of Virulent and Avirulent Strains ofPorphyromonas gingivalis

Abstract

We used Porphyromonas gingivalis gene microarrays to compare the total gene contents of the virulent strain W83 and the avirulent type strain, ATCC 33277. Signal ratios and scatter plots indicated that the chromosomes were very similar, with approximately 93% of the predicted genes in common, while at least 7% of them showed very low or no signals in ATCC 33277. Verification of the array results by PCR indicated that several of the disparate genes were either absent from or variant in ATCC 33277. Divergent features included already reported insertion sequences and ragB, as well as additional hypothetical and functionally assigned genes. Several of the latter were organized in a putative operon in W83 and encoded enzymes involved in capsular polysaccharide synthesis. Another cluster was associated with two paralogous regions of the chromosome with a low G؉C content, at 41%, compared to that of the whole genome, at 48%. These regions also contained conserved and species-specific hypothetical genes, transposons, insertion sequences, and integrases and were located adjacent to tRNA genes; thus, they had several characteristics of pathogenicity islands. While this global comparative analysis showed the close relationship between W83 and ATCC 33277, the clustering of genes that are present in W83 but divergent in or absent from ATCC 33277 is suggestive of chromosomal islands that may have been acquired by lateral gene transfer.The identification of virulent strains of pathogenic bacteria, and consequently their virulence genes, is a basic doctrine of the microbial pathogenesis field. Historically, identification has depended on phenotypic properties, biochemical activities, and immunological classifications. Increasingly, these tests have been replaced by genomic DNA-based analyses that can be successfully adapted to identify species, strains, and even mutants within strains. The availability of complete genome sequences for many bacterial pathogens has further increased the accuracy and specificity of such tests. A new addition to the existing repertoire of DNA analyses is comparative genome profiling using DNA microarrays, and this technology has been adapted to identify genes associated with pandemic strains of Vibrio cholerae (9) and to distinguish virulent strains of group A Streptococcus (30), Helicobacter pylori (4), and Salmonella species (6).Porphyromonas gingivalis is a gram-negative oral anaerobe associated with periodontal disease in adults. The organism is the most-studied oral pathogen, partly because it produces several virulence factors that can be isolated and studied biochemically (reviewed in reference 16) and partly because it is relatively easy to grow and manipulate genetically. According to animal models of disease, strains are classified as virulent and avirulent, and studies with bacterial strains and defined mutants have validated both the models and putative virulence factors (2, 3, 11). Strains of P. gingivalis have been differentiated by restriction fragment length polymorphism analysis of...

Quantitative proteomics of intracellular Porphyromonas gingivalis

“…About 7% of the genes in 33277 are reported to be highly divergent relative to the sequence strain, W83 [40]. As expected, these same highly divergent genes were under-represented in our dataset as expressed protein.…”

“…If we take into consideration the genome sequence differences between strains ATCC 33277 and W83 noted in the literature [40] and also the existence of several hundred annotated interposons and other mobile elements [10] that are typically not observed experimentally as proteins, our actual proteome qualitative coverage was on the order of 60% of the protein expressing ORFs. This was significantly higher coverage relative to other literature reports for intracellular pathogens.…”

Two-component signal transduction systems in oral bacteria

“…Therefore, the TCS was named HaeRS (for haemin). 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.…”

Genetic exchange and reassignment in Porphyromonas gingivalis

“…Ranging in size from 10 to 200 kb, pathogenicity islands often carry genes that encode integrases and transposases involved in DNA mobility, and they can be associated with tRNA genes, which are favoured sites for integration of foreign DNA [32]. This was demonstrated by Chen et al [32] when comparative whole-genome analysis of virulent (W83) and avirulent (ATCC 33277) strains of P. gingivalis was made.…”

“…Ranging in size from 10 to 200 kb, pathogenicity islands often carry genes that encode integrases and transposases involved in DNA mobility, and they can be associated with tRNA genes, which are favoured sites for integration of foreign DNA [32]. This was demonstrated by Chen et al [32] when comparative whole-genome analysis of virulent (W83) and avirulent (ATCC 33277) strains of P. gingivalis was made. In W83, one cluster of genes was associated with two paralogous regions of chromosomes with low G + C content that contained conserved and species-specific hypothetical genes, transposons, insertion sequences and integrases and was located close to tRNA genes, having many of the characteristics of pathogenicity islands acquired by lateral gene transfer.…”