Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83

Putative respiratory chain of Porphyromonas gingivalis

The electron transfer chain in Porphyromonas gingivalis, or periodontopathogens, has not yet been characterized. P. gingivalis, a strict anaerobic bacteria and the second colonizer of the oral cavity, is considered to be a major causal agent involved in periodontal diseases. Primary colonizers create a favorable environment for P. gingivalis growth by decreasing oxygen pressure. Oxygen does not appear to be the final electron acceptor of the respiratory chain. Fumarate and cytochrome b have been implicated as major components of the respiratory activity. However, the P. gingivalis genome shows many other enzymes that could be implicated in aerobic or nitrite respiration. Using bioinformatic tools and literature studies of respiratory pathways, the ATP synthesis mechanism from the sodium cycle and nutrients metabolism, the putative respirasome of P. gingivalis has been proposed.

The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information

The human oral microbiome is the most studied human microflora, but 53% of the species have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are known primarily from 16S rRNA sequence information. Sequence information tied solely to obscure isolate or clone numbers, and usually lacking accurate phylogenetic placement, is a major impediment to working with human oral microbiome data. The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with a body site-specific comprehensive database for the more than 600 prokaryote species that are present in the human oral cavity based on a curated 16S rRNA gene-based provisional naming scheme. Currently, two primary types of information are provided in HOMD—taxonomic and genomic. Named oral species and taxa identified from 16S rRNA gene sequence analysis of oral isolates and cloning studies were placed into defined 16S rRNA phylotypes and each given unique Human Oral Taxon (HOT) number. The HOT interlinks phenotypic, phylogenetic, genomic, clinical and bibliographic information for each taxon. A BLAST search tool is provided to match user 16S rRNA gene sequences to a curated, full length, 16S rRNA gene reference data set. For genomic analysis, HOMD provides comprehensive set of analysis tools and maintains frequently updated annotations for all the human oral microbial genomes that have been sequenced and publicly released. Oral bacterial genome sequences, determined as part of the Human Microbiome Project, are being added to the HOMD as they become available. We provide HOMD as a conceptual model for the presentation of microbiome data for other human body sites.

Database URL: http://www.homd.org

FimB regulates FimA fimbriation in Porphyromonas gingivalis

The periodontitis-associated pathogen Porphyromonas gingivalis colonizes and forms a biofilm in gingival crevices through fimbriae. It is known that the often-used strains ATCC 33277 and 381 produce long FimA fimbriae. We found a possible nonsense mutation within fimB, immediately downstream from fimA, coding a major subunit of FimA fimbriae of the strains. Indeed, P. gingivalis strains, except for ATCC 33277 and 381, universally expressed FimB, the gene product of fimB. Electron micrographs revealed that a FimB-restored strain had short and dense, "toothbrush"-like, FimA fimbriae. FimA overexpression elongated the fimbriae, whereas FimB overexpression shortened them. FimB restoration increased production of FimA and its accessory proteins. Thus, FimB regulates the length and expression of FimA fimbriae. Additionally, FimB restoration significantly reduced the release of FimA fimbriae from the cell surface, suggesting that FimB functions as an anchor of the fimbriae. The restoration enhanced adherent activity as well.

Characterization of hemin-binding protein 35 (HBP35) in Porphyromonas gingivalis: its cellular distribution, thioredoxin activity and role in heme utilization

Background

The periodontal pathogen Porphyromonas gingivalis is an obligate anaerobe that requires heme for growth. To understand its heme acquisition mechanism, we focused on a hemin-binding protein (HBP35 protein), possessing one thioredoxin-like motif and a conserved C-terminal domain, which are proposed to be involved in redox regulation and cell surface attachment, respectively.

Results

We observed that the hbp35 gene was transcribed as a 1.1-kb mRNA with subsequent translation resulting in three proteins with molecular masses of 40, 29 and 27 kDa in the cytoplasm, and one modified form of the 40-kDa protein on the cell surface. A recombinant 40-kDa HBP35 exhibited thioredoxin activity in vitro and mutation of the two putative active site cysteine residues abolished this activity. Both recombinant 40- and 27-kDa proteins had the ability to bind hemin, and growth of an hbp35 deletion mutant was substantially retarded under hemin-depleted conditions compared with growth of the wild type under the same conditions.

Conclusion

P. gingivalis HBP35 exhibits thioredoxin and hemin-binding activities and is essential for growth in hemin-depleted conditions suggesting that the protein plays a significant role in hemin acquisition.

Feasibility and therapeutic strategies of vaccines against Porphyromonas gingivalis

Periodontitis is a chronic infectious disease that is highly prevalent worldwide and is characterized by inflammation of the gums, and loss of connective tissue and bone support. The Gram-negative anerobic bacterium Porphyromonas gingivalis is generally accepted as the main etiological agent for chronic periodontitis. The objective of this paper is to elucidate the feasibility of achieving protection against periodontitis though immunization against P. gingivalis. Until now, animal studies have showed no complete protection against P. gingivalis. However, current knowledge about P. gingivalis structures could be applicable for further research to develop a successful licensed vaccine and alternative therapeutic strategies. This review reveals that a multicomponent vaccine against P. gingivalis, which includes structures shared among P. gingivalis serotypes, will be feasible to induce broad and complete protection.

Histidine kinase-mediated production and autoassembly of Porphyromonas gingivalis fimbriae

Porphyromonas gingivalis, a Gram-negative oral anaerobe, is strongly associated with chronic adult periodontitis, and it utilizes FimA fimbriae to persistently colonize and evade host defenses in the periodontal crevice. The FimA-related gene cluster (the fim gene cluster) is positively regulated by the FimS-FimR two-component system. In this study, comparative analyses between fimbriate type strain ATCC 33277 and fimbria-deficient strain W83 revealed differences in their fimS loci, which encode FimS histidine kinase. Using a reciprocal gene exchange system, we established that FimS from W83 is malfunctional. Complementation analysis with chimeric fimS constructs revealed that W83 FimS has a defective kinase domain due to a truncated conserved G3 box motif that provides an ATP-binding pocket. The introduction of the functional fimS from 33277 restored the production, but not polymerization, of endogenous FimA subunits in W83. Further analyses with a fimA-exchanged W83 isogenic strain showed that even the fimbria-deficient W83 retains the ability to polymerize FimA from 33277, indicating the assembly of mature FimA by a primary structure-dependent mechanism. It also was shown that the substantial expression of 33277-type FimA fimbriae in the W83 derivative requires the introduction and expression of the functional 33277 fimS. These findings indicate that FimSR is the unique and universal regulatory system that activates the fim gene cluster in a fimA genotype-independent manner.

FimR and FimS: biofilm formation and gene expression in Porphyromonas gingivalis

Porphyromonas gingivalis is a late-colonizing bacterium of the subgingival dental plaque biofilm associated with periodontitis. Two P. gingivalis genes, fimR and fimS, are predicted to encode a two-component signal transduction system comprising a response regulator (FimR) and a sensor histidine kinase (FimS). In this study, we show that fimS and fimR, although contiguous on the genome, are not part of an operon. We inactivated fimR and fimS in both the afimbriated strain W50 and the fimbriated strain ATCC 33277 and demonstrated that both mutants formed significantly less biofilm than their respective wild-type strains. Quantitative reverse transcription-real-time PCR showed that expression of fimbriation genes was reduced in both the fimS and fimR mutants of strain ATCC 33277. The mutations had no effect, in either strain, on the P. gingivalis growth rate or on the response to hydrogen peroxide or growth at pH 9, at 41 degrees C, or at low hemin availability. Transcriptome analysis using DNA microarrays revealed that inactivation of fimS resulted in the differential expression of 10% of the P. gingivalis genome (>1.5-fold; P < 0.05). Notably genes encoding seven different transcriptional regulators, including the fimR gene and three extracytoplasmic sigma factor genes, were differentially expressed in the fimS mutant.

Identification and Quantification of Genomic Repeats and Sample Contamination in Assemblies of 454 Pyrosequencing Reads

Contigs assembled from 454 reads from bacterial genomes demonstrate a range of read depths, with a number of contigs having a depth that is far higher than can be expected. For reference genome sequence datasets, there exists a high correlation between the contig specific read depth and the number of copies present in the genome. We developed a sequence of applied statistical analyses, which suggest that the number of copies present can be reliably estimated based on the read depth distribution in de novo genome assemblies. Read depths of contigs of de novo cyanobacterial genome assemblies were determined, and several high read depth contigs were identified. These contigs were shown to mainly contain genes that are known to be present in multiple copies in bacterial genomes. For these assemblies, a correlation between read depth and copy number was experimentally demonstrated using real-time PCR. Copy number estimates, obtained using the statistical analysis developed in this work, are presented. Per-contig read depth analysis of assemblies based on 454 reads therefore enables de novo detection of genomic repeats and estimation of the copy number of these repeats. Additionally, our analysis efficiently identified contigs stemming from sample contamination, allowing for their removal from the assembly.

Antimicrobial peptide inhibition of Porphyromonas gingivalis 381-induced hemagglutination is improved with a synthetic decapeptide

The effects of various antimicrobial peptides (AMPs) on disrupting the hemagglutinating ability of cellular components of the putative oral pathogen Porphyromonas gingivalis were examined. AMP inhibition of P. gingivalis 381-induced hemagglutination using vesicles (VES) or outer membrane (OM) preparations was determined within standardized hemagglutination assays using various mammalian erythrocytes. A synthetic decapeptide (KSL-W) and its truncated peptide analogs were evaluated and compared with selected classes of AMPs derived from naturally occurring innate defense peptides. All tested AMPs were effective in disrupting P. gingivalis-induced hemagglutination among tested erythrocytes, with the exception of magainin I and the truncated KSL-W analogs. LL-37 was generally the most potent followed by histatin 5. The synthetic decapeptide (KSL-W) was found to be similar to the histatin 8 peptide in terms of inhibitory effect. In addition, co-application assays (with selected oral-related AMPs+/-KSL-W) were employed to determine if co-application procedures would improve hemagglutination abrogation above that of oral-related AMPs alone. These experiments revealed that the KSL-W peptide improved hemagglutination inhibition above that of each of the oral-related peptides (histatin 5 and 8, LL-37) alone. Among mammalian erythrocytes, significant peptide-induced hemagglutination was observed for the cathelicidin class AMPs, LL-37 and indolicidin (>or=25 and >or=100 microM respectively). In contrast, KSL-W did not induce erythrocyte agglutination throughout any concentration range tested (0.1-1000 microM). Our results suggest that several AMPs are effective in disrupting P. gingivalis 381-induced hemagglutination and that the co-application of a small, synthetically derived peptide may serve to augment the role of local host AMPs engaged in innate defense.

Virulence genes of Porphyromonas gingivalis W83 in chronic periodontitis

OBJECTIVE

To identify virulence genes found in highly virulent strains of Porphyromonas gingivalis (P. gingivalis) among Chinese patients with chronic periodontitis and to evaluate the association of these virulence genes with clinical parameters and with periodontal tissue destruction.

MATERIAL AND METHODS

Suppression subtractive hybridization was applied to acquire short gene fragments harbored only in virulent strains of P. gingivalis W83. Eighteen genes, which were present in P. gingivalis W83 but absent from P. gingivalis ATCC 33277, were labeled with Cy5 and used as probes in DNA microarray hybridization to analyze DNA of P. gingivalis isolated from chronic periodontitis patients.

RESULTS

Spearman correlation analysis revealed 10 genes correlated with probing depth, clinical attachment loss, and tooth mobility (p<0.05).

CONCLUSION

These genes may provide an important clue towards our understanding the mechanism of occurrence and the development of periodontal disease.

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database

BACKGROUND

Porphyromonas gingivalis is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain P. gingivalis ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: AE015924]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: AP009380] and an analysis of differential abundance based on metabolic pathways rather than individual proteins.

RESULTS

Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized P. gingivalis within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription.

CONCLUSION

Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells provides a more energy rich environment compared to the extracellular milieu. Shifts in the production of cytotoxic fatty acids by intracellular P. gingivalis may play a role in virulence. Moreover, despite extensive genomic re-arrangements between strains W83 and 33277, there is sufficient sequence similarity at the peptide level for proteomic abundance trends to be largely accurate when using the heterologous strain annotated genome as the reference for database searching.

Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate

Porphyromonas gingivalis, previously classified as a strict anaerobe, can grow in the presence of low concentrations of oxygen. Microarray analysis revealed alteration in gene expression in the presence of 6 % oxygen. During the exponential growth phase, 96 genes were upregulated and 79 genes were downregulated 1.4-fold. Genes encoding proteins that play a role in oxidative stress protection were upregulated, including alkyl hydroperoxide reductase (ahpCF), superoxide dismutase (sod) and thiol peroxidase (tpx). Significant changes in gene expression of proteins that mediate oxidative metabolism, such as cytochrome d ubiquinol oxidase-encoding genes, cydA and cydB, were detected. The expression of genes encoding formate uptake transporter (PG0209) and formate tetrahydrofolate ligase (fhs) was drastically elevated, which indicates that formate metabolism plays a major role under aerobic conditions. The concomitant reduction of expression of a gene encoding the lactate transporter PG1340 suggests decreased utilization of this nutrient. The concentrations of both formate and lactate were assessed in culture supernatants and cells, and they were in agreement with the results obtained at the transcriptional level. Also, genes encoding gingipain protease secretion/maturation regulator (porR) and protease transporter (porT) had reduced expression in the presence of oxygen, which also correlated with reduced protease activities under aerobic conditions. In addition, metal transport was affected, and while iron-uptake genes such as the genes encoding the haemin uptake locus (hmu) were downregulated, expression of manganese transporter genes, such as feoB2, was elevated in the presence of oxygen. Finally, genes encoding putative regulatory proteins such as extracellular function (ECF) sigma factors as well as small proteins had elevated expression levels in the presence of oxygen. As P. gingivalis is distantly related to the well-studied model organism Escherichia coli, results from our work may provide further understanding of oxygen metabolism and protection in other related bacteria belonging to the phylum Bacteroidetes.

Porphyromonas gingivalis strain diversity

Porphyromonas gingivalis is implicated in the etiology of chronic periodontitis. Genotyping studies suggest that genetic variability exists among P. gingivalis strains; however, the extent of variability remains unclear and regions of variability remain largely unidentified. To assess P. gingivalis strain diversity, we previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type strains in clinical samples and identified 22 heteroduplex types. Additionally, we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of the strains. In the current study, heteroduplex analysis of the ISR was used to determine the worldwide genetic variability and distribution of P. gingivalis, and microarray-based comparative genomic hybridization (CGH) analysis was used to more comprehensively examine the variability of major heteroduplex type strains by using the entire genome. Heteroduplex analysis of clinical samples from geographically diverse populations identified 6 predominant geographically widespread heteroduplex types (prevalence, > or = 5%) and 14 rare heteroduplex types (prevalence, <2%) which are found in one or a few locations. CGH analysis of the genomes of seven clinically prevalent heteroduplex type strains identified 133 genes from strain W83 that were divergent in at least one of the other strains. The relatedness of the strains to one another determined on the basis of genome content (microarray) analysis was highly similar to their relatedness determined on the basis of ISR sequence analysis, and a striking correlation between the genome contents and disease-associated phenotypes of the strains was observed.

Identification of a gingipain-sensitive surface ligand of Porphyromonas gingivalis that induces Toll-like receptor 2- and 4-independent NF-kappaB activation in CHO cells

Porphyromonas gingivalis is a major periodontal pathogen that has the pathogenic proteinases Arg-specific gingipain and Lys-specific gingipain. We previously found that a cell surface component on P. gingivalis is able to induce Toll-like receptor 2 (TLR2)- and TLR4-independent signaling in 7.19 cells and that this component can be degraded by gingipains. In this study, we purified this component from the P. gingivalis gingipain-null mutant KDP136 and obtained two candidate proteins. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry analysis showed that the proteins, with molecular masses of 123 and 43 kDa, were encoded by PGN_0748 and PGN_0728 (pgm6), respectively, in the P. gingivalis ATCC 33277 genome sequence. The PGN_0748-encoded protein, which we refer to as gingipain-sensitive ligand A (GslA), reacted with antiserum that could effectively inhibit the activity of KDP136 to induce NF-kappaB activation in 7.19 cells, but Pgm6 did not. To further determine what protein is responsible for the NF-kappaB activation, we constructed gslA, pgm6, and pgm6 pgm7 deletion mutants from KDP136. When 7.19 cells were exposed to those mutants, the gslA deletion mutant did not induce NF-kappaB activation, whereas the pgm6 and pgm6 pgm7 deletion mutants did. Furthermore, NF-kappaB activation in 7.19 cells induced by KDP136 was partially inhibited by antiserum against a recombinant protein expressed from the 5'-terminal third of gslA. These results indicate that GslA is one of the factors that induce NF-kappaB activation in 7.19 cells. Interestingly, the gslA gene was present in four of seven P. gingivalis strains tested. This restricted distribution might be associated with the virulence potential of each strain.

Structural analysis of the core region of O-lipopolysaccharide of Porphyromonas gingivalis from mutants defective in O-antigen ligase and O-antigen polymerase

Porphyromonas gingivalis synthesizes two lipopolysaccharides (LPSs), O-LPS and A-LPS. Here, we elucidate the structure of the core oligosaccharide (OS) of O-LPS from two mutants of P. gingivalis W50, Delta PG1051 (WaaL, O-antigen ligase) and Delta PG1142 (O-antigen polymerase), which synthesize R-type LPS (core devoid of O antigen) and SR-type LPS (core plus one repeating unit of O antigen), respectively. Structural analyses were performed using one-dimensional and two-dimensional nuclear magnetic resonance spectroscopy in combination with composition and methylation analysis. The outer core OS of O-LPS occurs in two glycoforms: an "uncapped core," which is devoid of O polysaccharide (O-PS), and a "capped core," which contains the site of O-PS attachment. The inner core region lacks L(D)-glycero-D(l)-manno-heptosyl residues and is linked to the outer core via 3-deoxy-D-manno-octulosonic acid, which is attached to a glycerol residue in the outer core via a monophosphodiester bridge. The outer region of the "uncapped core" is attached to the glycerol and is composed of a linear alpha-(1-->3)-linked d-Man OS containing four or five mannopyranosyl residues, one-half of which are modified by phosphoethanolamine at position 6. An amino sugar, alpha-D-allosamine, is attached to the glycerol at position 3. In the "capped core," there is a three- to five-residue extension of alpha-(1-->3)-linked Man residues glycosylating the outer core at the nonreducing terminal residue. beta-D-GalNAc from the O-PS repeating unit is attached to the nonreducing terminal Man at position 3. The core OS of P. gingivalis O-LPS is therefore a highly unusual structure, and it is the basis for further investigation of the mechanism of assembly of the outer membrane of this important periodontal bacterium.

Quantitative PCR for genetic markers of human fecal pollution

Assessment of health risk and fecal bacterial loads associated with human fecal pollution requires reliable host-specific analytical methods and a rapid quantification approach. We report the development of quantitative PCR assays for quantification of two recently described human-specific genetic markers targeting Bacteroidales-like cell surface-associated genes. Each assay exhibited a range of quantification from 10 to 1 x 10(6) copies of target DNA. For each assay, internal amplification controls were developed to detect the presence or absence of amplification inhibitors. The assays predominantly detected human fecal specimens and exhibited specificity levels greater than 97% when tested against 265 fecal DNA extracts from 22 different animal species. The abundance of each human-specific genetic marker in primary effluent wastewater samples collected from 20 geographically distinct locations was measured and compared to quantities estimated by real-time PCR assays specific for rRNA gene sequences from total Bacteroidales and enterococcal fecal microorganisms. Assay performances combined with the prevalence of DNA targets in sewage samples provide experimental evidence supporting the potential application of these quantitative methods for monitoring fecal pollution in ambient environmental waters.

Anchoring and length regulation of Porphyromonas gingivalis Mfa1 fimbriae by the downstream gene product Mfa2

Porphyromonas gingivalis, a causative agent of periodontitis, has at least two types of thin, single-stranded fimbriae, termed FimA and Mfa1 (according to the names of major subunits), which can be discriminated by filament length and by the size of their major fimbrilin subunits. FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells. However, a P. gingivalis ATCC 33277-derived mutant deficient in mfa2, a gene downstream of mfa1, produced long filaments (10 times longer than those of the parent), easily detached from the cell surface, similar to FimA fimbriae. Longer Mfa1 fimbriae contributed to stronger autoaggregation of bacterial cells. Complementation of the mutant with the wild-type mfa2 allele in trans restored the parental phenotype. Mfa2 is present in the outer membrane of P. gingivalis, but does not co-purify with the Mfa1 fimbriae. However, co-immunoprecipitation demonstrated that Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells. Furthermore, immunogold microscopy, including double labelling, confirmed that Mfa2 was located on the cell surface and likely associated with Mfa1 fimbriae. Mfa2 may therefore play a role as an anchor for the Mfa1 fimbriae and also as a regulator of Mfa1 filament length. Two additional downstream genes (pgn0289 and pgn0290) are co-transcribed with mfa1 (pgn0287) and mfa2 (pgn0288), and proteins derived from pgn0289, pgn0290 and pgn0291 appear to be accessory fimbrial components.

Expression of peptidylarginine deiminase from Porphyromonas gingivalis in Escherichia coli: enzyme purification and characterization

Porphyromonas gingivalis peptidylarginine deiminase (PAD) catalyzes the deimination of peptidylarginine residues of various peptides to produce peptidylcitrulline and ammonia. P. gingivalis is associated with adult-onset periodontitis and cardiovascular disease, and its proliferation depends on secretion of PAD. We have expressed two recombinant forms of the P. gingivalis PAD in Escherichia coli, a truncated form with a 43-amino acid N-terminal deletion and the full-length form of PAD as predicted from the DNA sequence. Both forms contain a poly-His tag and Xpress epitope at the N-terminus to aid in detection and purification. The activities and stabilities of these two forms have been evaluated. PAD is cold sensitive; it aggregates within 30 min at 4 degrees C, and optimal storage conditions are at 25 degrees C in the presence of a reducing agent. PAD is not a metalloenzyme and does not need a cofactor for catalysis or stability. Multiple l-arginine analogs, various arginine-containing peptides, and free l-arginine were used to evaluate substrate specificity and determine kinetic parameters.

The gingipains: scissors and glue of the periodontal pathogen, Porphyromonas gingivalis

The anaerobic bacterium, Porphyromonas gingivalis, is associated with chronic periodontal disease (periodontitis or gum disease). The disease is not only the leading cause of tooth loss in the developed world, but is associated with a number of systemic diseases, such as cardiovascular disease and diabetes. The most potent virulence factors of this bacterium are the gingipains, three cysteine proteases that bind and cleave a wide range of host proteins. This article summarizes current knowledge of the structure and function of the enzymes, with a particular focus on what remains to be elucidated regarding the structure and function of the nonenzymatic adhesin domains of the high-molecular-weight forms of the proteases.

Characteristics of Bacteroides fragilis lacking the major outer membrane protein, OmpA

OmpA1 is the major outer membrane protein of the Gram-negative anaerobic pathogen Bacteroides fragilis. We identified three additional conserved ompA homologues (ompA2-ompA4) and three less homologous ompA-like genes (ompAs 5, 6 and 7) in B. fragilis. We constructed an ompA1 disruption mutant in B. fragilis 638R (WAL6 OmegaompA1) using insertion-mediated mutagenesis. WAL6 OmegaompA1 formed much smaller colonies and had smaller, rounder forms on Gram stain analysis than the parental strain or other unrelated disruption mutants. SDS-PAGE and Western blot analysis (with anti-OmpA1 IgY) of the OMP patterns of WAL6 OmegaompA1 grown in both high- and low-salt media did not reveal any other OmpA proteins even under osmotic stress. An ompA1 deletant (WAL186DeltaompA1) was constructed using a two-step double-crossover technique, and an ompA 'reinsertant', WAL360+ompA1, was constructed by reinserting the ompA gene into WAL186DeltaompA1. WAL186DeltaompA1 was significantly more sensitive to exposure to SDS, high salt and oxygen than the parental (WAL108) or reinsertant (WAL360+ompA1) strain. No significant change was seen in MICs of a variety of antimicrobials for either WAL6 OmegaompA1 or WAL186DeltaompA1 compared to WAL108. RT-PCR revealed that all of the ompA genes are transcribed in the parental strain and in the disruption mutant, but, as expected, ompA1 is not transcribed in WAL186DeltaompA1. Unexpectedly, ompA4 is also not transcribed in WAL186DeltaompA1. A predicted structure indicated that among the four OmpA homologues, the barrel portion is more conserved than the loops, except for specific conserved patches on loop 1 and loop 3. The presence of multiple copies of such similar genes in one organism would suggest a critical role for this protein in B. fragilis.

Proteomics of Porphyromonas gingivalis within a model oral microbial community

BACKGROUND

Porphyromonas gingivalis is a periodontal pathogen that resides in a complex multispecies microbial biofilm community known as dental plaque. Confocal laser scanning microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell quantitative proteomics, along with mutant construction and analysis, were conducted to investigate how P. gingivalis adapts to this three species community.

RESULTS

1156 P. gingivalis proteins were detected qualitatively during comparison of the three species model community with P. gingivalis incubated alone under the same conditions. Integration of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins were down-regulated and 89 proteins up-regulated. The proteomics results were inspected manually and an ontology analysis conducted using DAVID. Significant decreases were seen in proteins involved in cell shape and the formation of the cell envelope, as well as thiamine, cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-regulated in the community and an hmuR deficient mutant was deficient in three species community formation, but was unimpaired in its ability to form mono- or dual-species biofilms.

CONCLUSION

Collectively, these results indicate that P. gingivalis can assemble into a heterotypic community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for community structure.

The structurally similar, penta-acylated lipopolysaccharides of Porphyromonas gingivalis and Bacteroides elicit strikingly different innate immune responses

Lipid A structural modifications can substantially impact the host's inflammatory response to bacterial LPS. Bacteroides fragilis, an opportunistic pathogen associated with life-threatening sepsis and intra-abdominal abscess formation, and Bacteroides thetaiotaomicron, a symbiont pivotal for proper host intestinal tissue development, both produce an immunostimulatory LPS comprised of penta-acylated lipid A. Under defined conditions, Porphyromonas gingivalis, an oral pathogen associated with periodontitis, also produces an LPS bearing a penta-acylated lipid A. However, this LPS preparation is 100-1000 times less potent than Bacteroides LPS in stimulating endothelial cells. We analyzed Bacteroides and P. gingivalis lipid A structures using MALDI-TOF MS and gas chromatography to determine the structural basis for this phenomenon. Even though both Bacteroides and P. gingivalis lipid A molecules are penta-acylated and mono-phosphorylated, subtle differences in mass and fatty acid content could account for the observed difference in LPS potency. This fatty acid heterogeneity is also responsible for the peak "clusters" observed in the mass spectra and obfuscates the correlation between LPS structure and immunostimulatory ability. Further, we show the difference in potency between Bacteroides and P. gingivalis LPS is TLR4-dependent. Altogether, the data suggest subtle changes in lipid A structure may profoundly impact the host's innate immune response.

Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis

Infection, survival, and proliferation of pathogenic bacteria in humans depend on their capacity to impair host responses and acquire nutrients in a hostile environment. Among such nutrients is heme, a co-factor for oxygen storage, electron transport, photosynthesis, and redox biochemistry, which is indispensable for life. Porphyromonas gingivalis is the major human bacterial pathogen responsible for severe periodontitis. It recruits heme through HmuY, which sequesters heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR. Here we report that heme binding does not significantly affect the secondary structure of HmuY. The crystal structure of heme-bound HmuY reveals a new all-β fold mimicking a right hand. The thumb and fingers pinch heme iron through two apical histidine residues, giving rise to highly symmetric octahedral iron co-ordination. The tetrameric quaternary arrangement of the protein found in the crystal structure is consistent with experiments in solution. It shows that thumbs and fingertips, and, by extension, the bound heme groups, are shielded from competing heme-binding proteins from the host. This may also facilitate heme transport to HmuR for internalization. HmuY, both in its apo- and in its heme-bound forms, is resistant to proteolytic digestion by trypsin and the major secreted proteases of P. gingivalis, gingipains K and R. It is also stable against thermal and chemical denaturation. In conclusion, these studies reveal novel molecular properties of HmuY that are consistent with its role as a putative virulence factor during bacterial infection.

Pathogenic bacteria cause infection in humans as found in periodontitis, which is a chronic inflammation of the gums caused by Porphyromonas gingivalis. As part of the infective process, bacteria must acquire nutrients to survive and multiply at the infection site, and among such nutrients is heme. This is an iron-dependent co-factor of several indispensable enzymes and proteins. P. gingivalis liberates heme from host heme-binding proteins through the action of proteases and arranges its transport to the bacterial cell through two proteins, HmuY and HmuR. They grab free heme and transport it across the bacterial membrane into the cell, respectively. This function poses stringent conditions on these proteins regarding stability and resistance toward the host immune system. We report here that HmuY is very stable and that it displays a novel protein fold, which consists only of β-strands. It reminds us of a right hand, whose fingers trap heme. Once heme is bound, HmuY forms tetramers, which have the four heme-binding sites buried and thus protected from competing host heme-binding proteins. This feature also facilitates heme transport to HmuR and into the bacterial cell. All these data may help to develop new antibacterial agents at times in which resistance toward antibiotics, both at intensive healthcare stations and in the community, poses serious challenges to human health.

Identification and molecular characterization of tryptophanase encoded by tnaA in Porphyromonas gingivalis

Indole produced via the beta-elimination reaction of l-tryptophan by pyridoxal 5'-phosphate-dependent tryptophanase (EC 4.1.99.1) has recently been shown to be an extracellular and intercellular signalling molecule in bacteria, and controls bacterial biofilm formation and virulence factors. In the present study, we determined the molecular basis of indole production in the periodontopathogenic bacterium Porphyromonas gingivalis. A database search showed that the amino acid sequence deduced from pg1401 of P. gingivalis W83 is 45 % identical with that from tnaA of Escherichia coli K-12, which encodes tryptophanase. Replacement of the pg1401 gene in the chromosomal DNA with the chloramphenicol-resistance gene abolished indole production. The production of indole was restored by the introduction of pg1401, demonstrating that the gene is functionally equivalent to tnaA. However, RT-PCR and RNA ligase-mediated rapid amplification of cDNA ends analyses showed that, unlike E. coli tnaA, pg1401 is expressed alone in P. gingivalis and that the nucleotide sequence of the transcription start site is different, suggesting that the expression of P. gingivalis tnaA is controlled by a unique mechanism. Purified recombinant P. gingivalis tryptophanase exhibited the Michaelis-Menten kinetics values K(m)=0.20+/-0.01 mM and k(cat)=1.37+/-0.06 s(-1) in potassium phosphate buffer, but in sodium phosphate buffer, the enzyme showed lower activity. However, the cation in the buffer, K(+) or Na(+), did not appear to affect the quaternary structure of the enzyme or the binding of pyridoxal 5'-phosphate to the enzyme. The enzyme also degraded S-ethyl-l-cysteine and S-methyl-l-cysteine, but not l-alanine, l-serine or l-cysteine.

Verification of a topology model of PorT as an integral outer-membrane protein in Porphyromonas gingivalis

PorT is a membrane-associated protein shown to be essential for the maturation and secretion of a class of cysteine proteinases, the gingipains, from the periodontal pathogen Porphyromonas gingivalis. It was previously reported that PorT is located on the periplasmic surface of the inner membrane to function as a chaperone for the maturing proteinases. Our modelling suggested it to be an integral outer-membrane protein with eight anti-parallel, membrane-traversing beta-strands. In this report, the outer-membrane localization model was confirmed by the structural and functional tolerance of PorT to hexahistidine (6xHis) tag insertions at selected locations within the protein using site-directed mutagenesis. Interestingly, those PorT mutations adversely affecting gingipain secretion enhanced expression of the porT gene but at the same time suppressed the transcription of the gingipain rgpB gene. Further, PorT mutants deficient in gingipain activities produced significantly more di- and triaminopeptidase activities. PorT homologues have been found in restricted members of the Bacteroidetes phylum where there is potential for PorT to participate in the maturation and secretion of proteins with characteristic C-terminal domains (CTDs). Knowledge of the cellular localization of PorT will enable analysis of the role of this protein in a new secretory pathway for the export of gingipains and other CTD-class proteins.

Comparative transcriptomic analysis of Porphyromonas gingivalis biofilm and planktonic cells

BACKGROUND

Porphyromonas gingivalis in subgingival dental plaque, as part of a mature biofilm, has been strongly implicated in the onset and progression of chronic periodontitis. In this study using DNA microarray we compared the global gene expression of a P. gingivalis biofilm with that of its planktonic counterpart grown in the same continuous culture.

RESULTS

Approximately 18% (377 genes, at 1.5 fold or more, P-value < 0.01) of the P. gingivalis genome was differentially expressed when the bacterium was grown as a biofilm. Genes that were down-regulated in biofilm cells, relative to planktonic cells, included those involved in cell envelope biogenesis, DNA replication, energy production and biosynthesis of cofactors, prosthetic groups and carriers. A number of genes encoding transport and binding proteins were up-regulated in P. gingivalis biofilm cells. Several genes predicted to encode proteins involved in signal transduction and transcriptional regulation were differentially regulated and may be important in the regulation of biofilm growth.

CONCLUSION

This study analyzing global gene expression provides insight into the adaptive response of P. gingivalis to biofilm growth, in particular showing a down regulation of genes involved in growth and metabolic activity.

Metabolic network model of a human oral pathogen

The microbial community present in the human mouth is engaged in a complex network of diverse metabolic activities. In addition to serving as energy and building-block sources, metabolites are key players in interspecies and host-pathogen interactions. Metabolites are also implicated in triggering the local inflammatory response, which can affect systemic conditions such as atherosclerosis, obesity, and diabetes. While the genome of several oral pathogens has been sequenced, quantitative understanding of the metabolic functions of any oral pathogen at the system level has not been explored yet. Here we pursue the computational construction and analysis of the genome-scale metabolic network of Porphyromonas gingivalis, a gram-negative anaerobe that is endemic in the human population and largely responsible for adult periodontitis. Integrating information from the genome, online databases, and literature screening, we built a stoichiometric model that encompasses 679 metabolic reactions. By using flux balance approaches and automated network visualization, we analyze the growth capacity under amino-acid-rich medium and provide evidence that amino acid preference and cytotoxic by-product secretion rates are suitably reproduced by the model. To provide further insight into the basic metabolic functions of P. gingivalis and suggest potential drug targets, we study systematically how the network responds to any reaction knockout. We focus specifically on the lipopolysaccharide biosynthesis pathway and identify eight putative targets, one of which has been recently verified experimentally. The current model, which is amenable to further experimental testing and refinements, could prove useful in evaluating the oral microbiome dynamics and in the development of novel biomedical applications.

Response of Porphyromonas gingivalis to heme limitation in continuous culture

Porphyromonas gingivalis is an anaerobic, asaccharolytic, gram-negative bacterium that has essential requirements for both iron and protoporphyrin IX, which it preferentially obtains as heme. A combination of large-scale quantitative proteomic analysis using stable isotope labeling strategies and mass spectrometry, together with transcriptomic analysis using custom-made DNA microarrays, was used to identify changes in P. gingivalis W50 protein and transcript abundances on changing from heme-excess to heme-limited continuous culture. This approach identified 160 genes and 70 proteins that were differentially regulated by heme availability, with broad agreement between the transcriptomic and proteomic data. A change in abundance of the enzymes of the aspartate and glutamate catabolic pathways was observed with heme limitation, which was reflected in organic acid end product levels of the culture fluid. These results demonstrate a shift from an energy-efficient anaerobic respiration to a less efficient process upon heme limitation. Heme limitation also resulted in an increase in abundance of a protein, PG1374, which we have demonstrated, by insertional inactivation, to have a role in epithelial cell invasion. The greater abundance of a number of transcripts/proteins linked to invasion of host cells, the oxidative stress response, iron/heme transport, and virulence of the bacterium indicates that there is a broad response of P. gingivalis to heme availability.

The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins

Bacteria and archaea use distinct pathways for salvaging exogenous cobinamide (Cbi), a precursor of adenosylcobalamin (coenzyme B(12)). The bacterial pathway depends on a bifunctional enzyme with kinase and guanylyltransferase activities (CobP in aerobic adenosylcobalamin synthesizers) to convert adenosylcobinamide (AdoCbi) to AdoCbi-guanosine diphosphate (AdoCbi-GDP) via an AdoCbi-phosphate intermediate. Archaea lack CobP, and use a different strategy for the synthesis of AdoCbi-GDP. Archaea cleave off the aminopropanol group of AdoCbi using the CbiZ AdoCbi amidohydrolase to generate adenosylcobyric acid, which is converted to AdoCbi-phosphate by the CbiB synthetase, and to AdoCbi-GDP by the CobY guanylyltransferase. We report phylogenetic, in vivo and in vitro evidence that the genome of Rhodobacter sphaeroides encodes functional enzymes for Cbi salvaging systems of both bacterial and archaeal origins. Products of the reactions were identified by high-performance liquid chromatography, UV-visible spectroscopy and bioassay. The cbiZ genes of several bacteria and archaea restored Cbi salvaging in a strain of Salmonella enterica unable to salvage Cbi. Phylogenetic data led us to conclude that CbiZ is an enzyme of archaeal origin that was horizontally transferred to bacteria. Reasons why some bacteria may contain both types of Cbi salvaging systems are discussed.

Aggressive assembly of pyrosequencing reads with mates

MOTIVATION

DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a 'hybrid' approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.

RESULTS

Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data.

AVAILABILITY

The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.

Regulation of hemin binding proteins by a novel transcriptional activator in Porphyromonas gingivalis

One of the features of the periodontal pathogen Porphyromonas gingivalis is the presence of complex iron acquisition systems that include an hmuYRSTUV locus. HmuY and HmuR are hemin binding proteins required for P. gingivalis growth. Previous studies have demonstrated that expression of the hmu locus is regulated in response to environmental changes, such as growth phases. However, the mechanisms involved in hmu gene regulation are poorly understood. Here we report that a novel transcriptional activator, PG1237, is required for the expression of humY and humR, but not other iron acquisition-related genes, such as fetB and tlr, which also encode hemin binding proteins. Real-time reverse transcription-PCR analysis revealed that a mutation in the pg1237 gene decreased expression of hmuY and hmuR 149- and 25-fold, respectively, compared to that observed in the wild-type strain. In addition, differential expression of hmuY, hmuR, and the pg1237 gene was found to be quorum-sensing dependent, such that higher expression levels of these genes were observed when P. gingivalis was grown at a lower cell density, such as that seen during the early exponential growth phase. This work demonstrates the involvement of a novel transcriptional activator, PG1237, in expression of the hmu operon in a cell density-dependent fashion.

DNA repair of 8-oxo-7,8-dihydroguanine lesions in Porphyromonas gingivalis

The persistence of Porphyromonas gingivalis in the inflammatory environment of the periodontal pocket requires an ability to overcome oxidative stress. DNA damage is a major consequence of oxidative stress. Unlike the case for other organisms, our previous report suggests a role for a non-base excision repair mechanism for the removal of 8-oxo-7,8-dihydroguanine (8-oxo-G) in P. gingivalis. Because the uvrB gene is known to be important in nucleotide excision repair, the role of this gene in the repair of oxidative stress-induced DNA damage was investigated. A 3.1-kb fragment containing the uvrB gene was PCR amplified from the chromosomal DNA of P. gingivalis W83. This gene was insertionally inactivated using the ermF-ermAM antibiotic cassette and used to create a uvrB-deficient mutant by allelic exchange. When plated on brucella blood agar, the mutant strain, designated P. gingivalis FLL144, was similar in black pigmentation and beta-hemolysis to the parent strain. In addition, P. gingivalis FLL144 demonstrated no significant difference in growth rate, proteolytic activity, or sensitivity to hydrogen peroxide from that of the parent strain. However, in contrast to the wild type, P. gingivalis FLL144 was significantly sensitive to UV irradiation. The enzymatic removal of 8-oxo-G from duplex DNA was unaffected by the inactivation of the uvrB gene. DNA affinity fractionation identified unique proteins that preferentially bound to the oligonucleotide fragment carrying the 8-oxo-G lesion. Collectively, these results suggest that the repair of oxidative stress-induced DNA damage involving 8-oxo-G may occur by a still undescribed mechanism in P. gingivalis.

Surface components of Porphyromonas gingivalis

BACKGROUND AND OBJECTIVE

Research on Porphyromonas gingivalis, a periodontopathogen, has provided a tremendous amount of information over the last 20 years, which may exceed in part than that on other closely related members in terms of phylogenetic as well as proteomic criteria, including Bacteroides fragilis and B. thetaiotaomicron as major anaerobic, opportunistic pathogens in the medical field. In this minireview, we focused on recent research findings concerning surface components such as outer membrane proteins and fimbriae, of P. gingivalis.

MATERIAL AND METHODS

Elucidation of the surface components in P. gingivalis was especially difficult because outer membrane proteins are tightly bound to lipopolysaccharide and they are resistant to dissociation and separation from each other, even during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, unless samples are appropriately heated. In addition, P. gingivalis is asaccharolytic and therefore a potent proteolytic bacterium, another factor causing difficulty in research. The study of the surface components was carefully carried out considering these unique features in P. gingivalis when compared with other gram-negative bacteria, including Escherichia coli and Pseudomonas aeruginosa.

RESULTS

Separation of outer membrane proteins, and characterization of OmpA-like proteins and RagAB as major proteins, is described herein. Our recent findings on FimA and Mfa1 fimbriae, two unique appendages in this organism, and on their regulation of expression are also described briefly.

CONCLUSION

Surface components of P. gingivalis somehow have contact with host tissues and cells because of the outermost cell elements. Therefore, such bacterial components are potentially important in the occurrence of periodontal diseases.

Expression patterns of genes induced by oxidative stress in Porphyromonas gingivalis

INTRODUCTION

Porphyromonas gingivalis, a gram-negative anaerobic bacterium, is a major periopathogen whose transmission from host to host involves exposure to atmospheric oxygen. P. gingivalis contains genetic factors that function in an oxidative stress response, but their expression has not been analyzed during exposure to atmospheric oxygen. The aim of this study was to obtain a better understanding of atmospheric adaptation of P. gingivalis.

METHODS

The aerotolerance of wild-type and oxyR mutant P. gingivalis strains were determined, and quantitative polymerase chain reaction was performed to analyze gene expression patterns in response to exposure to atmospheric oxygen. The analyzed P. gingivalis genes encoded proteins involved in oxidative response (oxyR, ahpC-F, batA, dps, ftn, tpx) as well as several major virulence factors (hagA, hagB, hagE, rgpA, rgpB, hem).

RESULTS

Our results demonstrated a critical role for the oxyR gene in the aerotolerance of P. gingivalis. The ahpC-F, batA, and hem genes were slightly overexpressed (between 1.65-fold and 2-fold) after exposure to atmospheric oxygen compared to anaerobic conditions. The level of transcription of dps, ftn, tpx, and rgpA genes increased more than 2.5-fold, and the expression of ahpC-F, dps, ftn, and tpx was partially or completely OxyR-dependent.

CONCLUSION

A different transcription pattern of P. gingivalis genes was observed, depending on the stimulus of oxidative stress. We present new evidence that the expression of tpx, encoding a thiol peroxidase, is partially OxyR-dependent and is induced after atmospheric oxygen exposure.

The Phylogeny and Signature Sequences Characteristics ofFibrobacteres,Chlorobi, andBacteroidetes

Fibrobacteres, Chlorobi, and Bacteroidetes (FCB group) comprise three main bacterial phyla recognized on the basis of 16S rRNA trees. Presently, there are no distinctive biochemical or molecular characteristics known that can distinguish these bacteria from other bacterial phyla. The relationship of these bacteria to other phyla is also not known. This review describes many signatures, consisting of defined and conserved inserts in widely distributed proteins, that provide distinctive molecular markers for these groups of bacteria. These signatures serve to clarify the evolutionary relationship between members of the FCB group, and to other bacterial phyla. A 4 aa insert in DNA Gyrase B (GyrB) and a 45 aa insert in the SecA proteins are uniquely shared by various Bacteroidetes species. The insert in GyrB is present in all Bacteroidetes species (>100) covering different orders and families, indicating that it is a distinctive characteristic of the group. Three signatures consisting of an 18 aa insert in ATPase alpha-subunit, an 8-9 aa insert in the FtsK protein and a 1 aa insert in the UvrB protein are commonly shared only by the Bacteroidetes and Chlorobi homologs providing evidence that these two groups are specifically related to each other. Two additional inserts in the RNA polymerase beta'-subunit (5-7 aa) and Serine hydroxymethyl-transferase (14-16 aa), which are commonly present in various Bacteroidetes, Chlorobi, and Fibrobacteres homologs, but not any other bacteria, provide evidence that these groups shared a common ancestor exclusive of all other bacteria. The FCB groups of bacteria are indicated to have diverged from this common ancestor in the following order: Fibrobacteres --> Chlorobi --> Bacteriodetes. The inferences from signature sequences are strongly supported by phylogenetic analyses. These observations suggest that the FCB groups of bacteria should be placed in a single phylum rather than three distinct phyla. Signature sequences in a number of other proteins provide evidence that the FCB group of bacteria diverged at a similar time as the Chlamydiae group, and that the Spirochetes and Aquificales groups are its closest relatives.

Functional analysis of the thioredoxin domain in Porphyromonas gingivalis HBP35

Periodontitis is one of the most common oral diseases in humans. This caused by infection by the oral bacterium Porphyromonas gingivalis. Our strategy to prevent this infection is to establish a passive immunization system in which endogenous antibodies can be applied directly to neutralize virulent factors associated with this bacterium. We focused our attention on the P. gingivalis 35 kDa surface protein, or HBP35, since this protein is involved not only in the coaggregation with oral miroflora but also in hemin binding. In addition, nucleotide sequencing of the gene, hbp35, coding for this protein revealed the presence of a catalytic center for thioredoxin, and we further attempted to characterized the protein by amino acid substitution. A total of four Cys residues were substituted for Ser residues by combining the simple method for site-directed mutagenesis and the heterodimer system, an approach designed to construct chimeric plasmids readily. Native and mutagenized hbp35 were introduced into the Eschericha coli dsbA mutant strain, JCB 572, defective in both alkaline phosphatase and motile activities due to inefficient disulfide bond formation. Transformant harboring the native hbp35 could complement the dsbA mutation, suggesting a role of disulfide bond formation of this protein in P. gingivalis cells. Possible roles of the Cys residues in complementation are discussed.

Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis

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).