Diversity analysis of genes encoding Mfa1 fimbrial components in Porphyromonas gingivalis strains

Kotaro Sakae; Keiji Nagano; Miyuna Furuhashi; Yoshiaki Hasegawa

doi:10.1371/journal.pone.0255111

Abstract

Porphyromonas gingivalis, a gram-negative anaerobic bacterium, is associated with the development of periodontal disease. The genetic diversity in virulence factors, such as adhesive fimbriae, among its strains affects the bacterial pathogenicity. P. gingivalis generally expresses two distinct types of fimbriae, FimA and Mfa1. Although the genetic diversity of fimA, encoding the major FimA fimbrilin protein, has been characterized, the genes encoding the Mfa1 fimbrial components, including the Mfa1 to Mfa5 proteins, have not been fully studied. We, therefore, analyzed their genotypes in 12 uncharacterized and 62 known strains of P. gingivalis (74 strains in total). The mfa1 genotype was primarily classified into two genotypes, 53 and 70. Additionally, we found that genotype 70 could be further divided into two subtypes (70A and 70B). The diversity of mfa2 to mfa4 was consistent with the mfa1 genotype, although no subtype in genotype 70 was observed. Protein structure modeling showed high homology between the genotypes in Mfa1 to Mfa4. The mfa5 gene was classified into five genotypes (A to E) independent of other genotypes. Moreover, genotype A was further divided into two subtypes (A1 and A2). Surprisingly, some strains had two mfa5 genes, and the 2^nd mfa5 exclusively occurred in genotype E. The Mfa5 protein in all genotypes showed a homologous C-terminal half, including the conserved C-terminal domain recognized by the type IX secretion system. Furthermore, the von Willebrand factor domain at the N-terminal was detected only in genotypes A to C. The mfa1 genotypes partially correlated with the ragA and ragB genotypes (located immediately downstream of the mfa gene cluster) but not with the fimA genotypes.

Citation: Sakae K, Nagano K, Furuhashi M, Hasegawa Y (2021) Diversity analysis of genes encoding Mfa1 fimbrial components in Porphyromonas gingivalis strains. PLoS ONE 16(7): e0255111. https://doi.org/10.1371/journal.pone.0255111

Editor: Özlem Yilmaz, Medical University of South Carolina, UNITED STATES

Received: April 17, 2021; Accepted: July 8, 2021; Published: July 26, 2021

Copyright: © 2021 Sakae et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the manuscript and its Supporting Information files.

Funding: The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Introduction

Porphyromonas gingivalis, a gram-negative anaerobic bacterium, is associated with the development and progression of periodontal disease [1]. This bacterium is a keystone pathogen that has a crucial influence on a microbial niche [2, 3]. As such, P. gingivalis leads the periodontal microbiota to dysbiosis, an imbalanced state of the microbiota, which then evokes inflammation in gingival tissues, although the bacterium is only present in a small quantity [2, 3].

P. gingivalis expresses various virulence factors, most notably fimbria, which functions to form a multi-species biofilm and colonizes the periodontal tissue [4]. At least two distinct types of fimbriae are expressed by the bacterium, namely, the FimA and Mfa1 fimbriae (Yoshimura, 2009 #1402). Other virulence factors also include gingipain, a trypsin-like protease, which causes tissue damage in the host [5]. Furthermore, capsules and lipopolysaccharides are known to facilitate immune evasion and inflammation induction, respectively [5]. However, P. gingivalis is also present in healthy subjects and shows divergent properties in pathology, indicating that there is genetic diversity in its virulence factors [6–8].

The fimA gene was the first to be identified as responsible for the diversity in P. gingivalis [9–11]. The fimA gene encodes a major fimbrilin protein (FimA), which polymerizes into a filament of FimA fimbriae [12]. The fimA gene has been classified into six genotypes (I to V, and Ib) based on either PCR using genotype-specific primers, or on the presence or absence of restriction enzyme cleavage [8]. However, genotype Ib is now unified into genotype I because of their similar antigenicity and overall DNA sequences [13, 14]. Studies from many countries have reported that genotypes II and IV are predominantly detected in patients with severe periodontitis, whereas genotype I is prevalent in healthy or mild periodontitis subjects [8, 15, 16]. However, genotype I is also reportedly detected at a high frequency in severe periodontitis [17, 18]. Moreover, a previous study showed no association between the fimA genotype and bacterial pathogenicity [19]. The discrepancies between these results indicate that the pathogenic diversity in P. gingivalis cannot be explained by the fimA genotype alone.

We previously found two genotypes in the mfa1 gene, which encodes the major fimbrilin of Mfa1 fimbriae, and called them 53 (kDa) and 70 (kDa) genotypes based on the apparent molecular weight of the Mfa1 proteins encoded by the gene [20, 21]. The DNA and amino acid sequences of the representative strains of genotypes 53 (strain Ando) and 70 (strain ATCC 33277) showed only 52.6% and 38.1% similarity, respectively. Additionally, these two genotypes exhibit differential antigenicity [20]. However, we did not detect any relationship between the mfa1 genotype and the severity of periodontal disease [21].

The FimA and Mfa1 proteins polymerize to form a filamentous structure by a similar mechanism [22]; via proteolytic processing by a signal peptidase and gingipain to yield the mature forms. Then, the C-terminal donor strands of the incoming monomer extend and bind to the hydrophobic groove of the prior monomer [23, 24]. This is known as the donor-strand exchange mechanism in the assembly of Escherichia coli fimbriae [25], but unlike in P. gingivalis, chaperone and usher proteins are absent, whereas digestion with protease (gingipain) is involved in maturation [22]. This proteinase-mediated donor-strand exchange mechanism, currently seen only in the class Bacteroidia, is called type V fimbriae [23]. FimA and Mfa1 fimbriae have four additional accessory proteins, FimB to FimE, and Mfa2 to Mfa5, respectively [4]. Genomic analysis of the ATCC 33277 type strain revealed that the genes encoding the FimA and Mfa1 fimbriae-associated proteins form respective clusters: fimB to fimE arrange immediately downstream of fimA, while mfa1 to mfa5 sequentially arrange (Fig 1). FimB and Mfa2 also show similar biogenesis and function [23, 26–28]. During maturation, they are digested by a signal peptidase, but not by gingipain. They localize at the base of the respective fimbriae and function to anchor the fimbrial filament to the bacterial body [26, 27]. Additionally, integration of FimB and Mfa2 into the respective fimbriae terminates fimbrial elongation [26, 27]. During maturation of FimC, FimD, FimE, Mfa3, and Mfa4, digestion with gingipain is necessary [23, 28–32]. They function as adhesins and facilitate fimbrial assembly [23, 28–33]. Unlike the other proteins described above, Mfa5 first translocates to the periplasmic space via a signal peptide and then to the outer membrane by the type IX secretion system (T9SS) [32]. T9SS secretes a bacterial protein that is uniquely found in the phylum Bacteroidetes [34]. Proteins recognized by the T9SS have a characteristic motif called the C-terminal domain (CTD) [35], which is found in Mfa5 of ATCC 33277 [32]. Recently, X-ray crystallography revealed that Mfa5 contained one von Willebrand factor (VWF) domain and two Ig-like domains in the N-terminal half [36]. It also showed that a loop structure called ARM2 is adjunct to the VWF domain. Furthermore, the observed formation of isopeptide bonds (between Lys¹¹¹ and Asn⁵¹⁸ of Mfa5 in ATCC 33277) reportedly only occurs in gram-positive bacteria such as streptococci [36].

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Fig 1. Gene map of the fim, mfa, and rag gene clusters of a type strain (ATCC 33277) of P. gingivalis.

There are distances between the fim gene cluster (fimA to fimE), as well as mfa (mfa1 to mfa5) and rag (ragA and ragB) gene clusters. The fimB gene is placed in parentheses because there is a nonsense mutation in ATCC 33277. Arrows depict gene directions from 5՛ to 3՛.

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The rag gene cluster contains the ragA and ragB genes immediately downstream of the mfa gene cluster in ATCC 33277 (Fig 1). They encode proteins localized in the outer and inner membranes, respectively, and associate with each other to function in nutrient uptake [37–39]. It has also been shown to stimulate innate immunity and induce inflammation [40]. There are four genetic polymorphisms in ragA and ragB, and, therefore, four potential associations between the genotypes and bacterial pathogenicity [37].

Previously, we did not determine the mfa1 genotype in 12 of the 84 strains of P. gingivalis in western blot and PCR analyses [20]. This suggested the existence of a novel mfa1 genotype. Therefore, in the present study we analyzed the draft genome of the 12 strains by next-generation sequencing (NGS) to define their mfa1 genotypes. We also analyzed the genomes of the additional 62 strains of P. gingivalis published in the expanded Human Oral Microbiome Database (eHOMD) (http://www.homd.org/) to examine the genomic diversity in the mfa gene cluster. Lastly, we analyzed the correlation of genetic diversity in the mfa gene cluster with those in the fim and rag gene clusters.

Materials and methods

P. gingivalis strains

We analyzed the genomic data of 12 unsequenced strains (222, 1436, 1439, B42, B158, D83T3, EM3, JKG9, JKG10, Kyudai-3, Kyudai-4, and TV14) [13] as described below. We also used genomic information from 62 sequenced strains (381, 11A, 13_1, 15_9, 3_3, 381OKJP, 3A1, 7BTORR, 84_3, A7436, A7A1-28, AFR5B1, AJW4, Ando, ATCC 33277, ATCC 49417, CP3, F0185, F0566, F0568, F0569, F0570, H3, HG66, JCVI SC001, KCOM 2796, KCOM 2797, KCOM 2798, KCOM 2799, KCOM 2800, KCOM 2801, KCOM 2802, KCOM 2803, KCOM 2804, KCOM 2805, KCOM 3001, KCOM 3131, MP4-504, SJD11, SJD12, SJD2, SJD4, SJD5, SU60, TDC 60, UBA8864, W4087, W50, W83, WW2096, WW2842, WW2866, WW2881, WW2885, WW2903, WW2931, WW2952, WW3039, WW3040, WW3102, WW5019, and WW5127) published on the eHOMD website.

NGS analysis

We analyzed the genome sequence of 12 P. gingivalis strains whose mfa1 genotypes have not been determined as described above [20] (Table 1). The strains were maintained on Brucella HK agar (Kyokuto Pharmaceutical Industrial, Tokyo, Japan) supplemented with 5% rabbit blood, defibrinated at 37°C under anaerobic conditions. A black pigmented colony was inoculated and cultivated in the GAM broth, Modified (Nissui Pharmaceutical, Tokyo, Japan) to collect the bacterial cells. Chromosomal DNA was extracted using the Wizard Genomic DNA Purification Kit (Promega Corporation, Madison, WI, USA) and subjected to NGS analysis. The draft genome sequences were analyzed by Filgen (Nagoya, Japan), and 150-bp paired-end sequences generated by NovaSeq (Illumina, San Diego, CA, USA) were de novo assembled using ABySS version 2.2.4 [41] using the bioinformatics software OmicsBox (BioBam Bioinformatics S.L., Valencia, Spain). The optimal k-mer values were determined using the total length of the assembled sequence as an index.

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Table 1. Basic information of genome-sequencing of 12 strains in this study.

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Bioinformatics

Bioinformatics analysis was performed using the programs listed in Table 2. Detection of mfa, fim, and rag gene clusters was performed using BLAST on the web. When the 12 strains sequenced in this study were analyzed, we used BLAST with the “Align two or more sequences” enabled. The assembly data including all contigs were entered in a box for “query sequence,” and a probe sequence was entered in “subject sequence.” Then, the contig containing the probe sequence was obtained for further analysis. When the strains published in the eHOMD site were analyzed, the target genes were detected using a tool of “Genome Viewer” in the eHOMD site, and the contig containing the target sequence was obtained. The eHOMD shows open reading frames (ORFs) and amino acid sequences deduced from the ORFs. However, we found different ORFs between the strains, although their DNA sequences were almost identical. We modified the ORFs to align the start codon among the strains and then analyzed the DNA sequences. We determined the bacterial species through the DNA sequences of 16S rRNA and multilocus sequence typing analysis (MLST) of seven genes of P. gingivalis including pepO, gpdxJ, hagB, recA, mcmA, pga, and ftsQ in the PubMLST site [7]. A phylogenetic tree was constructed using TreeView X through a multiple sequence alignment analysis using ClustalΩ version 1.2.2. The genotype was classified based on the phylogenetic distance and cluster formation; when the phylogenetic distance between the genes was less than 0.1, they were classified into a single genotype. However, even when the phylogenetic distance was less than 0.1, genes were classified into different genotype considering the genotype of the adjacent genes. Furthermore, if there were multiple distinct clusters within a genotype, they were classified as subtypes.

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Table 2. Program and web site of bioinformatics used in this study.

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Additionally, the genotypes of fimA, ragA, and ragB were named according to the same terminology as those in previous papers: fimA was classified as genotype I to V [8], whereas ragA and ragB were classified into genotypes 1 to 4 (or ragA-1/ragB-1 to ragA-4/ragB-4) [42]. A signal peptide was predicted using SignalP 5.0. SWISS-MODEL analysis was used for protein structure homology modeling based on the X-ray crystal structures deposited in the Protein Data Bank (PDB). The X-ray crystal structures of the mature forms of Mfa1 [28, 43], Mfa2 [28, 43], Mfa3 [28, 29], and Mfa4 [23, 30] proteins, and the N-terminal portion of the Mfa5 protein [36] have been published at the PDB site previously. All structural data were based on the DNA sequence of ATCC 33277.

Results

Draft genome sequencing and detection of the mfa1 gene in the 12 unsequenced strains

NGS analysis produced a draft genome sequence of the 12 strains whose mfa1 genotypes were not determined previously [20]. The results are summarized in Table 1 with GenBank accession numbers. All strains were assembled into approximately 100 contigs, with a total length comparable to the genome sizes of strains ATCC 33277 (2,354,886 bp [44]) and W83 (2,343,476 bp [45]). They also showed high-quality values of N₅₀ with more than 33,000. We confirmed the presence of P. gingivalis through the DNA sequences of 16S rRNA and MLST analysis with 99.5 to 100% identity.

BLAST searches of the mfa gene cluster from the draft genomes of the 12 strains are shown in Table 3. The mfa1 gene was detected in 11 strains, but not in strain 222. Strain 222 showed only the latter half of the mfa5, and traA and traB genes encoding conjugative transposon proteins upstream of the truncated mfa5 gene. A possible nonsense mutation in mfa1 was detected in B158, Kyudai-4, and TV14, which are unlikely to express the Mfa1 protein. In D83T3 and Kyudai-3, although the entire mfa1 gene exists, the insertion sequence (IS) could be seen immediately downstream of it, and the contig was different from mfa2 and beyond. In JKG10, the first half of the mfa1 gene was not detected because the gene was located at the end of a contig, and it was therefore not possible to determine whether the full length of the gene existed. The rag and fim gene clusters were detected in all the strains, including 222.

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Table 3. Genotypes in the mfa, rag, and fim gene clusters.

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Detection of the mfa, rag, and fim gene clusters

In addition to the 12 strains described above, the mfa, rag, and fim gene clusters were extracted from the genome data of 62 P. gingivalis strains published on eHOMD (Table 3). The mfa1, mfa2, mfa3, mfa4, mfa5, ragA, and ragB genes were tandemly arranged in this order when both the mfa and rag gene clusters were detected in a contig. Surprisingly, there were strains possessing two mfa5 genes with a tandem arrangement. Hereafter, the first and second mfa5 genes are called mfa5-1 and mfa5-2, respectively. In the fim gene cluster, fimA to fimE were also arranged in sequence in all but two strains that contained the incomplete gene.

Genetic diversity in the mfa gene cluster

Genetic diversity was phylogenetically analyzed using ClustalΩ. The mfa1 gene was primarily classified into two genotypes, 53 and 70, as reported previously [20, 21] (Table 3 and Fig 2). Additionally, two cluster formations were observed in genotype 70. Here, we refer to them as genotypes 70A and 70B. The mfa2, mfa3, and mfa4 genes were classified into two genotypes consistent with those of mfa1, although genotype 70 was not divided into subtypes (Table 3; S1–S3 Figs). Additionally, the phylogenetic distance of mfa2 to mfa4 was less than that of mfa1; in particular, mfa2 showed high homogeneity among the strains.

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Fig 2. Phylogenetic tree of the mfa1 gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The mfa1 gene is primarily classified into genotypes 53 and 70. Additionally, genotype 70 forms two clusters, called genotypes 70A and 70B.

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The classification of mfa5 was completely different from that of mfa1 to mfa4. It was primarily classified into five genotypes, A to E (Table 3 and Fig 3). Additionally, genotype A showed two clusters, called genotypes A1 and A2. The gene length between the genotypes differed by more than double in some instances (Table 4): 2,946 to 3,747 in genotype A (including genotypes A1 and A2); 4,595 bp in genotype B; 5,049 bp in genotype C; 4,020 bp in genotype D; and 6,615 bp in genotype E (except for 6,614 of KCOM 2798 because of missing a nucleotide). Intriguingly, when 2 mfa5 genes were detected, the first (mfa5-1) and second (mfa5-2) genotypes were exclusively genotypes A2 and E, respectively.

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Fig 3. Phylogenetic tree of the mfa5 gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The mfa5 gene is primarily classified into 5 genotypes of A, B, C, D, and E. Additionally, genotype A forms 2 clusters, called genotypes A1 and A2. Strain names appending with either #1 or #2 indicate the first and second mfa5, respectively.

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Table 4. The mfa5 genotype and gene length.

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Protein structure and sequence analyses of Mfa1 to Mfa5

The protein structures of Mfa1 to Mfa5 between different genotypes were predicted and comparatively analyzed with SWISS-MODEL using the X-ray crystal structure data based on the gene information of ATCC 33277 as a template.

In the Mfa1 protein maturation of ATCC 33277, precursor peptides undergo removal of Arg⁴⁹ at the N-terminus during processing, including digestion with a signal peptidase and gingipain [46]. Therefore, we submitted the mature forms of the amino acid sequences deleting the N-terminal peptide corresponding to the Arg⁴⁹ of respective genotypes of 53 (Ando), 70A (ATCC 33277), and 70B (JKG9) to SWISS-MODEL analysis. Mfa1 of genotype 70A naturally showed a high concordance rate (QMEAN value) in the overall structure (Fig 4). The structural model of genotype 70B also showed very high concordance. Genotype 53 had low QMEAN values overall, but the β-barrel structure, important for structure determination, and the donor-strand exchange mechanism was significantly conserved.

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Fig 4. Protein structure homology-modeling of Mfa1.

The mature form of the amino acid sequences of genotypes 53 (Ando), 70A (ATCC 33277), and 70B (JKG9) were subjected to SWISS-MODEL analysis. Homology modeling was performed using Mfa1 of ATCC 33277 (5nf3.1.A in PDB) as a template. The quality of protein structure models is indicated by qualitative model energy analysis (QMEAN): blue and red indicate good and bad specific feature quality scores, respectively.

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Mfa2 is not processed by gingipain [28, 43], and SignalP 5.0 predicted that a signal peptide before Ser²⁸ was removed to yield the mature form. Mfa3 and Mfa4 are removed up to Arg⁴³ and Arg⁵⁴, respectively, by gingipain to yield the mature form [46]. These three protein structures of genotypes 53 (Ando) and 70 (ATCC 33277) showed a highly similar tertiary structure, as expected from the substantial homology of the primary structures (S4–S6 Figs).

In Mfa5, the primary structures were first analyzed (Fig 5). In all genotypes, the N-terminal signal peptide was predicted with high probability, and the CTD motif at the C-terminus was also conserved, though with two different sequence types (GAYVVSLQSPATSSNVRKVVVN and GAYIVHLQNAFTNDVHKVLVEY). Additionally, all genotypes contained homologous sequences in the C-terminal half. However, the VWF domain with the ARM2 loop and two Ig-like domains in the N-terminal half were detected only in four genotypes: A1, A2, B, and C. In these genotypes, the amino acid residues (Lys and Asn) involved in isopeptide bond formation were also located near the same positions in the four genotypes. Notably, an additional Ig-like domain was detected in genotype C. The tertiary structure of the N-terminal part, including VWF and 2 Ig-like domains, were highly conserved in genotypes A, B, and C (S7 Fig). Additionally, no similarity was detected in the N-terminal amino acid sequences between genotypes D and E; the N-terminal amino acid sequences of Mfa5 of TDC60 (genotype D) and the 2^nd Mfa5 of W83 (genotype E) showed only 10% identity. Furthermore, BLAST did not find homologous genes in the N-terminal half of genotypes D and E.

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Fig 5. Domain arrangement of the Mfa5 protein in respective genotypes.

Domain arrangements were designed based on the amino acid sequences deduced from the mfa5 gene of the representative strain of each genotype. The N- to C-terminal of the sequence is shown from left to right. The black box on the far-left side is the predicted signal peptide. Light and dark blue are Ig-like domains, called D2 and D3 domains in the paper published by Heidler et al. [36]. Genotype C has an additional Ig-like domain. The pink is the von Willebrand factor A domain, green (with a triangle) is ARM2, and gray at the C-terminal is the CTD. The CTD was classified into two types: light (GAYVVSLQSPATSSNVRKVVVN) and dark (GAYIVHLQNAFTNDVHKVLVEY) gray. Yellow is a common region among all genotypes. A1, ATCC 33277; A2, the first mfa5 (mfa5-1) of W83; B, the first mfa5 (mfa5-1) of SU60; C, WW5127; D, TDC60; E, the second mfa5 (mfa5-2) of W83.

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Genetic diversity in the rag gene cluster, and its correlation to the mfa gene cluster

The ragA gene was classified into four genotypes (ragA-1 to ragA-4), as reported previously [42] (Table 3 and S8 Fig). The classification of ragB completely matched that of ragA, as described previously [42] (Table 3 and S9 Fig). The ragA/ragB genes were present immediately downstream of the mfa gene cluster when the clusters were detected in the same contig. A relationship between the mfa1 and ragA/ragB genotypes was observed: 20 strains with genotype-53 mfa1 (detected for both of the mfa1 and ragA/ragB genes) showed no detection of ragA-4, while detected ragA-1, ragA-2, and ragA-3 in 8 (40%), 4 (20%), and 8 strains (40%), respectively. On the other hand, strains with 70A-genotype mfa1 (38 strains) showed a low detection rate of ragA-1 in 3 (7.9%), while substantially detected ragA-2, ragA-3, and ragA-4 in 13 strains (34.2%), 8 strains (21%), and 14 strains (36.8%), respectively. In strains with the 70B genotypes of mfa1, all six strains correlated with ragA-2. No correlation was observed between the genotypes A1, A2, and E of mfa5 with the ragA/ragB genotypes. However, although the sample number was small, genotypes C and D of mfa5 correlated to ragA-4 with high frequency: in three of four, and in two of four strains, respectively.

The rag gene cluster is followed by rgpA, which encodes gingipain in ATCC 33277 (Fig 1). However, the genes at this position were diverse among the strains, and other genes were detected, annotated as outer membrane proteins, lipoproteins, and hypothetical proteins. Additionally, no genetic diversity has been reported for rgpA [47].

Genetic diversity in the fim gene cluster and its correlation with the mfa gene cluster

The fimA gene was classified as genotypes I to V, as previously reported (Table 3 and S10 Fig). The fimB gene showed an almost homogenous sequence (Table 3 and S11 Fig). The fimC, fimD, and fimE genes were divided into two genotypes with high consistency, respectively referred to as genotypes A and B (Table 3, and S12–S14 Figs). Genotype B was present in only 13/74 strains, respectively in fimA genotypes I (2/21), II (1/38), III (1/4), IV (7/9), and V (2/2) strains, thus showing a high incidence of genotype B in fimA genotypes IV and V. No correlation was found between either the mfa1 and fimA genotypes, or the mfa5 and fimA genotypes.

Discussion

This study primarily examined the genetic diversity of the mfa1 to mfa5 genes encoding the Mfa1 fimbrial components of P. gingivalis. We first determined the mfa1 genotype in the 12 strains of P. gingivalis in which the mfa1 genotype had not been determined previously [20]. Of these, 11d out of 12 strains had genotype 70 of mfa1, and their mfa1 gene sequences contained multiple mismatched bases compared to the primers used for PCR in the previous study, retrospectively indicating unsuccessful PCR. The remaining strain 222 likely misses mfa1. It is also evident now that the previous western blotting failed to detect the Mfa1 protein in strains B158, Kyudai-4, and TV14 likely due to nonsense mutation in mfa1 preventing its expression [20]. Moreover, low protein expression and differential antigenicity might decrease the sensitivity of western blotting.

In addition to the above 12 strains, the genomic information of 62 strains of P. gingivalis published on the eHOMD site was used to analyze the genetic diversity in the mfa, rag, and fim gene clusters. We first examined the gene arrangement on the chromosome and found the mfa and rag gene clusters arranged consecutively when the genes in both clusters were all present in a contig. However, the genes downstream of ragB were diverse and appeared to be discontinuous. Additionally, the strains with the 2 mfa5 genes often showed a defective assembly of the genes, possibly because there was a homologous sequence between the two mfa5 genes (symbol X in Table 3). The fimA to fimE genes were detected in a cluster in all strains except the two strains.

Although the mfa1 gene was primarily classified into genotypes 53 and 70 previously, we found the possibility that genotype 70 can be further divided into subtypes 70A and 70B (Fig 2). However, the protein structural modeling by SWISS-MODEL analysis showed a significantly high homology between genotypes 70A and 70B (Fig 4). The mfa2, mfa3, and mfa4 genes were classified into two genotypes, which were consistent with the mfa1 genotypes, although genotype 70 from mfa2 to mfa4 was not further divided. This suggests that mfa1 to mfa4 develop during synchronization. However, it should be noted that the differences between the genotypes of mfa2 are very small, and the degree of diversity of mfa3 and mfa4 is less than that of mfa1. Furthermore, Mfa1 fimbriae were normally expressed even when mfa1 was replaced with a different genotype [20]. Briefly, the mfa1-deficient mutant of ATCC 33277 (genotype 70A) restored Mfa1 fimbriae by introducing mfa1 from Ando (genotype 53) in trans. This shows that mfa2, an anchor and length regulator [26], and both mfa3 and mfa4 are useful for fimbrial assembly [28–32] in different genotypes. The high conservation of the protein structures of Mfa1 to Mfa4 by SWISS-MODEL analysis also supports this result.

On the other hand, mfa5 showed a classification that was completely different from that of the other mfa genes. It was classified into five genotypes from A to E, and genotype A was further divided into subtypes A1 and A2 (Fig 3). The genes also showed considerable differences in gene length between the different genotypes (Table 4). Surprisingly, there was a substantial number of strains holding two mfa5 genes tandemly, and the first (mfa5-1) and second (mfa5-2) were exclusively genotypes A2 and E, respectively (Table 3). All genotypes showed the conserved C-terminal half and possessed CTD, indicating that Mfa5 is transported to the cell surface by T9SS, regardless of the genotype (Fig 5). However, N-terminals containing VWF domain, ARM2 loop, and the characteristic isopeptide bond were detected only in genotypes A1, A2, B, and C, whereas genotypes D and E did not have the N-terminal part. The binding site of the VWF domain in Mfa5 (of ATCC 33277, mfa5-genotype A1) was predicted to be blocked by an extended structure [36], and its function in the VWF domain remains unknown. On the other hand, it has been shown that a mutant strain expressing Mfa5 lacking the VWF domain reduced Mfa1-fimbrial expression, and the defective Mfa5 was no longer incorporated into the fimbrial structure [32]. However, Heidler et al. [36] indicated that a fatal mutation might occur in the overall structure of the defective Mfa5 lacking the VWF, and the function of the VWF domain alone might not be able to be examined. We are interested in the expression of Mfa1 fimbriae in a strain expressing Mfa5, encoded by the genotype-D mfa5. It would be also useful to examine fimbrial expression in a mutant strain deleted with genotype-A2 mfa5 from a strain with both A2- and E-genotypes mfa5. Additionally, the SU60 strain possesses mfa5 with genotype B and seems to have the secondary mfa5 (mfa5-2), although the sequences have not been fully read. Therefore, the genotype of mfa5-2 still needs to be determined. Heidler et al. [36] claimed that the mfa5 gene might be transferred from streptococci because of the homology between the Ma5 and streptococcal adhesins (RrgA and GBS104); however, this finding could not explain the genetic diversity of the mfa5. It also could not explain why all genotypes of mfa5 had the CTD found only in the phylum Bacteroidetes. Furthermore, it has been reported that Mfa1 fimbriae recognize SspB expressed on the cell surface of Streptococcus gordonii, which is the predominant bacterium in oral biofilms [48]. However, this examination was performed only using ATCC 33277, and should therefore be confirmed using strains expressing Mfa1 fimbriae composed of the proteins encoded by different genotypes of mfa1 to mfa5.d.

The ragA/ragB genes were classified into four genotypes, as previously reported, and both genotypes were completely in agreement. An association between the genotypes of ragA/ragB and mfa1 was observed; The ragA-4 genotype was absent in strains with genotype-53 mfa1, and ragA-1 rarely detected in strains with genotype-70A mfa1. Additionally, all six strains with genotype-70B mfa1 showed ragA-2. Thus, ragA-4 was only detected in strains with the genotype-70A mfa1. It is not surprising that the genotypes of the mfa1 and raga/ragB genes showed a relationship as both gene clusters were always tandemly arranged; however, the genetic diversity of mfa5 between them showed no relationship.

The fimA was classified into genotypes I to V, as previously reported. Additionally, to our knowledge this is the first report of 2 genotypes in fimC to fimE. We also showed that fimB was highly conserved in P. gingivalis, similar to mfa2, both of which have similar functions. The majority of fimC to fimE were classified as genotype A, while genotype B was detected in fimA-genotypes IV and V with high frequency, suggesting that there is a relationship between the genotypes of fimA, fimC, fimD, and fimE. Given the high pathogenicity of the fimA-genotype IV [8, 15, 16], we are interested in the association between genotype B in fimC to fimE, and bacterial pathogenicity. However, no association was found between the mfa1 and fimA genotypes or the mfa5 and fimA genotypes.

Conclusions

The mfa1 gene was classified into two genotypes, 53 and 70, although genotype 70 could be further divided into two subtypes. The genotypes of mfa2, mfa3, and mfa4 were consistent with those of mfa1. The classification of mfa5 was independent and mfa5 was classified into five genotypes and two subtypes. Surprisingly, there were strains with two mfa5 genes. All mfa5 genes have a common C-terminal part, including CTD, but not always VWF in the N-terminal portion. There seems to be a relationship between the mfa1 genotype and the ragA/ragB genotypes, but not with the fimA genotype. Future studies should focus on the association between the genotypes of accessory proteins, such as Mfa5, and pathogenicity in P. gingivalis.

Supporting information

S1 Fig. Phylogenetic tree of the mfa2 gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The mfa2 gene is primarily classified into genotypes 53 and 70.

https://doi.org/10.1371/journal.pone.0255111.s001

(TIF)

S2 Fig. Phylogenetic tree of the mfa3 gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The mfa3 gene is primarily classified into genotypes 53 and 70.

https://doi.org/10.1371/journal.pone.0255111.s002

(TIF)

S3 Fig. Phylogenetic tree of the mfa4 gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The mfa4 gene is primarily classified into genotypes 53 and 70.

https://doi.org/10.1371/journal.pone.0255111.s003

(TIF)

S4 Fig. Protein structure homology-modeling of Mfa2.

The mature form of the amino acid sequences of genotypes 53 (Ando) and 70 (ATCC 33277) were subjected to SWISS-MODEL analysis. Homology modeling was performed using the Mfa2 of ATCC 33277 (5nfi.1.A in PDB) as a template. The quality of protein structure models is indicated by qualitative model energy analysis (QMEAN): blue and red indicate good and bad quality specific feature scores, respectively.

https://doi.org/10.1371/journal.pone.0255111.s004

(TIF)

S5 Fig. Protein structure homology-modeling of Mfa3.

The mature form of the amino acid sequences of genotypes 53 (Ando) and 70 (ATCC 33277) were subjected to SWISS-MODEL analysis. Homology modeling was performed using Mfa3 of ATCC 33277 (5nf4.1.A in PDB) as a template. The quality of protein structure models is indicated by qualitative model energy analysis (QMEAN): blue and red indicate good and bad quality specific feature scores, respectively.

https://doi.org/10.1371/journal.pone.0255111.s005

(TIF)

S6 Fig. Protein structure homology-modeling of Mfa4.

The mature form of the amino acid sequences of genotypes 53 (Ando) and 70 (ATCC 33277) were subjected to SWISS-MODEL analysis. Homology modeling was performed using the Mfa4 of ATCC 33277 (4rdb.1.A in PDB) as a template. The quality of protein structure models is indicated by qualitative model energy analysis (QMEAN): blue and red indicate good and bad quality specific feature scores, respectively.

https://doi.org/10.1371/journal.pone.0255111.s006

(TIF)

S7 Fig. Protein structure homology-modeling of Mfa5.

The mature form of the amino acid sequences of genotypes A1 (ATCC 33277), B (SU60), and C (WW5127) were subjected to SWISS-MODEL analysis. Homology modeling was computed using Mfa4 of ATCC 33277 (6to1.1.A in PDB) as a template. The quality of protein structure models is indicated by qualitative model energy analysis (QMEAN): blue and red indicate good and bad quality specific feature scores, respectively. There is a possible missing nucleotide or misreading in mfa5-1 of SU60. This strain is the only genotype B. To add genotype B to this analysis, the sequence was modified with reference to the sequence of ATCC 3377 (“T” added between the 277^th and 278^th DNA).

https://doi.org/10.1371/journal.pone.0255111.s007

(TIF)

S8 Fig. Phylogenetic tree of the ragA gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The ragA gene is classified into genotypes 1–4.

https://doi.org/10.1371/journal.pone.0255111.s008

(TIF)

S9 Fig. Phylogenetic tree of the ragB gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The ragB gene is classified into genotypes 1–4.

https://doi.org/10.1371/journal.pone.0255111.s009

(TIF)

S10 Fig. Phylogenetic tree of the fimA gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The fimA gene was classified into genotypes I–V.

https://doi.org/10.1371/journal.pone.0255111.s010

(TIF)

S11 Fig. Phylogenetic tree of the fimB gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The fimB gene showed a homogeneous cluster.

https://doi.org/10.1371/journal.pone.0255111.s011

(TIF)

S12 Fig. Phylogenetic tree of the fimC gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The fimC gene is classified into genotypes A and B.

https://doi.org/10.1371/journal.pone.0255111.s012

(TIF)

S13 Fig. Phylogenetic tree of the fimD gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The fimD gene is classified into genotypes A and B.

https://doi.org/10.1371/journal.pone.0255111.s013

(TIF)

S14 Fig. Phylogenetic tree of the fimE gene.

A phylogenetic tree was constructed with TreeView X through a multiple sequence alignment analysis using ClustalΩ. The fimE gene was classified into genotypes A and B.

https://doi.org/10.1371/journal.pone.0255111.s014

(TIF)

Acknowledgments

We thank Filgen Inc. for their instruction on the NGS analysis. We would like to thank Editage (www.editage.com) for English language editing.

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Figures

Abstract

Introduction

Materials and methods

P. gingivalis strains

NGS analysis

Bioinformatics

Results

Draft genome sequencing and detection of the mfa1 gene in the 12 unsequenced strains

Detection of the mfa, rag, and fim gene clusters

Genetic diversity in the mfa gene cluster

Protein structure and sequence analyses of Mfa1 to Mfa5

Genetic diversity in the rag gene cluster, and its correlation to the mfa gene cluster

Genetic diversity in the fim gene cluster and its correlation with the mfa gene cluster

Discussion

Conclusions

Supporting information

S1 Fig. Phylogenetic tree of the mfa2 gene.

S2 Fig. Phylogenetic tree of the mfa3 gene.

S3 Fig. Phylogenetic tree of the mfa4 gene.

S4 Fig. Protein structure homology-modeling of Mfa2.

S5 Fig. Protein structure homology-modeling of Mfa3.

S6 Fig. Protein structure homology-modeling of Mfa4.

S7 Fig. Protein structure homology-modeling of Mfa5.

S8 Fig. Phylogenetic tree of the ragA gene.

S9 Fig. Phylogenetic tree of the ragB gene.

S10 Fig. Phylogenetic tree of the fimA gene.

S11 Fig. Phylogenetic tree of the fimB gene.

S12 Fig. Phylogenetic tree of the fimC gene.

S13 Fig. Phylogenetic tree of the fimD gene.

S14 Fig. Phylogenetic tree of the fimE gene.

Acknowledgments

References