Development of novel oligonucleotide probes for seven Actinomyces species and their utility in supragingival plaque analysis

OBJECTIVE

The traditional, biochemical and enzymatic methods of identifying Actinomyces species are frequently confounded by the similar phenotypic characteristics shared by the different members of this genus. Therefore, we developed novel species-specific oligonucleotide probes to accurately speciate seven pathogenic Actinomyces species, namely, Actinomyces bovis, A. gerencseriae, A. israelii, A. meyeri, A. naeslundii, A. odontolyticus and A. viscosus.

METHODS

A pair of universal primers and seven 15- to 19-base oligonucleotide probes with a tail of 20 thymidines on the 5' end were developed. The variable regions of 16S ribosomal DNA of 36 strains of Actinomyces belonging to the above species were amplified and labeled with digoxigenin, and an oligonucleotide-DNA hybridization assay was performed to examine the specificity and sensitivity of these probes.

RESULTS

All seven, newly developed probes were specific and sensitive, and accurately detected 36 reference and wild type strains belonging to Actinomyces species, without cross-reactions. The probe for A. naeslundii detected all strains belonging to the genospecies 1 (12 strains) and catalase-negative genospecies 2 (four strains); it failed to detect catalase-positive A. naeslundii genospecies 2 (previous A. viscosus serotype II) (two strains). However, the latter strains of catalase-positive A. naeslundii genospecies 2 were correctly detected by the probe developed for A. viscosus. The new probes were then field tested using supragingival plaque samples from 28 healthy preschool children. Whilst A. odontolyticus was detected in almost all samples (96.4%), A. gerencseriae, A. meyeri, catalase-negative A. naeslundii and catalase-positive A. naeslundii genospecies 2 were detected in < 50% samples.

CONCLUSION

We conclude that the developed oligonucleotide probes, complementary to the variable regions of 16S rDNA, would be of potential value for differentiating Actinomyces spp. in clinical samples from the oral cavity and other ecosystems where such species may abound.

Different type 1 fimbrial genes and tropisms of commensal and potentially pathogenic Actinomyces spp. with different salivary acidic proline-rich protein and statherin ligand specificities

Actinomyces spp. exhibit type 1 fimbria-mediated adhesion to salivary acidic proline-rich proteins (PRPs) and statherin ligands. Actinomyces spp. with different animal and tissue origins belong to three major adhesion types as relates to ligand specificity and type 1 fimbria genes. (i) In preferential acidic-PRP binding, strains of Actinomyces naeslundii genospecies 1 and 2 from human and monkey mouths displayed at least three ligand specificities characterized by preferential acidic-PRP binding. Slot blot DNA hybridization showed seven highly conserved type 1 fimbria genes (orf1- to -6 and fimP) in genospecies 1 and 2 strains, except that orf5 and orf3 were divergent in genospecies 1. (ii) In preferential statherin binding, oral Actinomyces viscosus strains of rat and hamster origin (and strain 19246 from a human case of actinomycosis) bound statherin preferentially. DNA hybridization and characterization of the type 1 fimbria genes from strain 19246 revealed a homologous gene cluster of four open reading frames (orfA to -C and fimP). Bioinformatics suggested sortase (orfB, orf4, and part of orf5), prepilin peptidase (orfC and orf6), fimbria subunit (fimP), and usher- and autotransporter-like (orfA and orf1 to -3) functions. Those gene regions corresponding to orf3 and orf5 were divergent, those corresponding to orf2, orf1, and fimP were moderately conserved, and those corresponding to orf4 and orf6 were highly conserved. Restriction fragment length polymorphism analyses using a fimP probe separated human and monkey and rat and hamster strains into phylogenetically different groups. (iii) In statherin-specific binding, strains of A. naeslundii genospecies 1 from septic and other human infections displayed a low-avidity binding to statherin. Only the orf4 and orf6 gene regions were highly conserved. Finally, rat saliva devoid of statherin bound bacterial strains avidly irrespective of ligand specificity, and specific antisera detected either type 1, type 2, or both types of fimbria on the investigated Actinomyces strains.

The diversity and distribution of the predominant ribotypes of Actinomyces naeslundii genospecies 1 and 2 in samples from enamel and from healthy and carious root surfaces of teeth

The bacterial communities associated with root caries are highly diverse and undergo succession during lesion formation. Consequently, root caries is said to have a polymicrobic etiology, typified by variation in the predominant species among samples from different lesions. Despite the polymicrobic etiology, A. naeslundii genospecies 1 and 2 (previously A. viscosus) have consistently been shown to be associated with root caries in humans; they predominate in some lesions and have been suggested to play a significant role in the disease. Several genetic variants of A. naeslundii are known to be present among the oral A. naeslundii population of an individual. The current study was initiated to explore the possibility that a variant in these A. naeslundii populations had characteristics which made it best fitted to colonize or promote root-surface caries lesions. Using ribotyping to detect variants, we tested the hypothesis that 'a ribotype of A. naeslundii best fitted to the environment would be selected and predominate in the A. naeslundii population of lesions'. Samples of plaque from enamel, normal root surfaces, plaque overlying the lesion, and material from within the lesion were taken from nine patients with soft root caries. The flora from 14 lesions and 9 enamel sites was analyzed on selective and non-selective media, and A. naeslundii genospecies were identified by serology. We ribotyped 972 isolates, showing 54 different patterns. Between 6 and 20 ribotypes were isolated from eight of nine patients. In general, each site from a patient showed a similar distribution of ribotypes. These results do not support the hypothesis and suggest that any phenotypic characters that allow A. naeslundii genospecies 1 and 2 to colonize or contribute to the formation of root-caries lesions are common among strains identified by ribotyping.

Synthesis and function of Actinomyces naeslundii T14V type 1 fimbriae require the expression of additional fimbria-associated genes

The nucleotide sequence of the chromosomal DNA flanking the Actinomyces naeslundii (formerly A. viscosus) T14V type 1 fimbrial structural subunit gene (fimP) was determined. Six open reading frames (ORFs), in the order 5' ORF3, ORF2, ORF1,fimP, ORF4, ORF5, ORF6 3', were identified. ORF1 encoded a protein of 408 amino acid residues (Mr = 39,270) and had significant sequence homology with the A. naeslundii T14V type 1 and A. naeslundii WVU45 type 2 fimbrial structural subunits. An in-frame fusion of ORF1 to the malE gene of the expression vector, pMAL-c2, yielded a protein that was immunostained with antibodies raised against the maltose binding protein and A. naeslundii T14V whole bacteria. Digestion of the fusion protein with factor Xa released a protein (apparent molecular mass of 34 kDa) that was immunostained only with the antibody directed against A. naeslundii T14V whole bacterial cells. Integration plasmids carrying a kanamycin resistance gene (kan) that was used to substitute for ORF1 or for DNA fragments internal to the coding region of the other five ORFs were used to transform A. naeslundii T14V. Neither type 1 fimbriae nor the 65-kDa fimbrial structural subunit was detected in mutants obtained by allelic replacement of ORF1 or ORF2. Mutants obtained by allelic replacement of ORF3 or ORF4 expressed only the 65-kDa fimbrial structural subunit. These mutants did not bind, in vitro, to proline-rich proteins that serve as the receptors for Actinomyces type 1 fimbriae. In contrast, a mutant in which the integration plasmid DNA had been inserted at a site close to the carboxyl terminus of ORF6 expressed type 1 fimbriae and had adherence properties similar to those observed in the wild-type strain. These results demonstrate the existence of additional genes near fimP that are likely to be involved in the synthesis and function of cell surface fimbriae of A. naeslundii T14V.

In vitro models that support adhesion specificity in biofilms of oral bacteria

Adhesion to adsorbed pellicles and interspecies co-adhesion to form plaque biofilms involve selective interactions of bacterial adhesins with specific receptors. Our laboratory has devised in vitro assays for co-adhesion between Actinomyces naeslundii and Streptococcus oralis or Porphyromonas gingivalis on saliva-coated mineral and hexadecane droplet substrata. P. gingivalis structures significant for co-adhesion with A. naeslundii include surface vesicles and fimbriae. A family of arginine-specific cysteine proteinases in vesicles may be involved in adherence to bacteria, to host cells, and to matrix proteins. New research from several laboratories has found that such proteinases are processed from genes encoding polyproteins containing both proteinase and hemagglutinin domains. In addition to enzyme-substrate recognition, bacterial adhesion is often determined by specific protein-peptide and lectincarbohydrate recognition. A. naeslundii--salivary prolinerich protein, S. gordonii--salivary alpha-amylase, and Treponema denticola--matrix protein recognition are examples of the former. Co-adhesion of A. naeslundii and S. oralis is an example of the latter. Lactose can selectively desorb A. naeslundii cells from mixed biofilms with S. oralis, a demonstration of the significance of specificity. Although non-specific forces are probably secondary to stereochemical fit in determining the selective range of surfaces that bacteria have evolved to recognize and bind, they probably help stabilize non-covalent bonds within aligned, complementary domains.

Detection of Actinomyces species using nonradioactive riboprobes coupled with polymerase chain reaction

We have been focusing our attention on the detection and identification of oral bacteria which are frequently associated with periodontal disease. In previous studies, Actinomyces species-specific riboprobes were generated and used to identify this microorganism. However, problems lie in the low sensitivity of this method. We have developed a novel system for the detection of Actinomyces species using nonradioactive riboprobes coupled with polymerase chain reaction (PCR) in this study. This system employs two procedures; initially, DNA fragments specific for the target microorganism are amplified by PCR, and these specific fragments are further hybridized with nonradioactive riboprobes. PCR analysis using chromosomal DNA isolated from Actinomyces species including laboratory strains, clinical isolates, and Actinomyces naeslundii (ATCC 12104) indicated the presence of the predicted common 756-bp fragment, a portion of the sialidase gene. These amplified DNA fragments were effectively visualized by hybridization with the digoxigenin-labeled riboprobes corresponding to the internal region of the amplified sialidase gene. With this system, approximately three orders of magnitude less chromosomal DNA was sufficient for the detection of specific microorganisms compared to the conventional riboprobe systems.

[Adherent mechanism of the mutans of Actinomyces viscosus T14V]

Three mutans of Actionmyces viscous T14V lacking type1 (5951), type 2 (5519) and both types of fimbriae (147) were selected in this study. We compared the ability of their adsorption to the test-tube wall, the result of the cellular coaggregation between these mutant strains and Streptococcus sanguis 34, Streptococcus sanguis black bova, Streptococcus mutans ingbritte, Streptococcus sobrinus 6715 and analysed the chemical characterization of cell walls of the three mutans. We found that the specific fimbriae and cell hydrophobicities had great effect on the bacteria adsorption or coaggregation.

Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes

Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.

Acid production by Actinomyces viscosus of root surface caries and non-caries origin during glycogen synthesis and degradation at different pH levels

Actinomyces viscosus strains, freshly isolated from root surface caries lesions and intact root surfaces, were studied for their glycogen synthetic and degradative activities at pH 4.5, 5.0, and 7.0 in a pH-stat. At all three pH levels, root caries origin of A. viscosus synthesized up to three times as much glycogen compared to non-root caries origin. Since root caries origin of A. viscosus strains initially synthesized large amounts of glycogen, a longer period of time was required to deplete this polymer, resulting in an extended period of acid production, even at pH 4.5 and pH 5.0. This study suggests that the ability of A. viscosus of root caries origin to synthesize large quantities of glycogen and subsequently degrade this stored polymer slowly with acid production, at acidic pH levels, may play an important role in the root caries process.

Cloning, sequencing and expression of the sialidase gene from Actinomyces viscosus DSM 43798

Chromosomal DNA from Actinomyces viscosus was digested with restriction endonucleases and the fragments ligated with pUC-vectors were used to transform Escherichia coli cells. Clones bearing the required sialidase gene were detected by spraying the colonies with the fluorogenic sialidase substrate MU-Neu5Ac. The identity of the cloned sialidase was confirmed after the 5700-fold enrichment and comparison with the purified enzyme of A. viscosus. Both sialidases were identical with regard to molecular mass, substrate specificity tested with sialyllactoses, and the inhibition of their activity by heterologous antisialidase antibodies. The sequenced insert (EMBL accession number X62276) revealed a mol% G + C of 68.2, typical for A. viscosus. An open reading frame of 2739 bp follows a sequence with dyad symmetry and an AG-rich region, and codes for 913 amino acids representing a molecular mass of 113 kDa. The conserved amino acid sequence [Ser-X-Asp-X-Gly-X-Thr-Trp] typical for bacterial sialidases was found at five positions in the predicted amino acid sequence. The gene of this enzyme is expressed by E. coli, despite the low relatedness of both species.

Isolation of a neuraminidase gene from Actinomyces viscosus T14V

A genomic library of Actinomyces viscosus T14V DNA in lambda gt11 was screened for expression of neuraminidase activities. Four recombinant clones were detected that gave blue fluorescence upon incubation with a fluorogenic substrate, 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid. Of these, two were identical, and all of the neuraminidase-positive clones shared a common 3.4-kbp DNA region. Expression of the enzyme activities in Escherichia coli carrying the cloned DNA was independent of the lacZ promoter of the vector. Maxicell analysis revealed that the 3.4-kbp DNA insert directed synthesis of a protein with an apparent molecular mass of 100,000 Da. The protein from cell extracts of E. coli clones migrated as a single band that stained for enzyme activity after electrophoresis in a nondissociating polyacrylamide gel. Moreover, human erythrocytes incubated previously with cell lysates from neuraminidase-positive E. coli were hemagglutinated by Actinomyces spp. The enzyme expressed by E. coli was active on substrates containing alpha-2,3 and alpha-2,6 ketosidic linked sialyl residues. Similar substrate specificities were obtained for both the extracellular and cell-associated neuraminidases from A. viscosus T14V. The 3.4-kbp insert hybridized to DNA fragments in a Southern blot containing A. viscosus T14V chromosomal DNA that had been digested with various restriction endonucleases. Data from hybridization studies show that A. viscosus T14V contains a single copy of the neuraminidase gene.