Introduction

Helicobacter pylori is a highly prevalent human pathogen infecting >50% of the population worldwide1,2 and is a causative factor of chronic gastritis, peptic ulcer and gastric cancer3,4. H. pylori is also characterized by its remarkable ability to persistently colonize its host. The need for H. pylori to adapt to the hostile, highly variable human gastric environment whilst having to subvert and evade host immune responses underpins its marked inter-strain genetic diversity. Phase variation, the high-frequency reversible on/off switching of gene expression5, is one of the major mechanisms employed by H. pylori to achieve genetic variation. Phase variable genes typically contain simple tandem DNA repeats within the open reading frame or promoter region. The reversible loss or gain of these repeats, mediated by slipped strand mispairing, can alter promoter specificity or cause frame-shift mutations that lead to inactivation or truncation of the resultant gene product. We previously reported that several clinically important bacterial pathogens, including H. pylori, express phase variable N6-adenosine type III DNA methyltransferases (Mod) that contribute to global changes in gene expression6,7,8,9,10,11. The target genes regulated by these phase variable DNA methyltransferases are collectively referred to as phase variable regulons, or phasevarions. Phasevarion-associated DNA methyltranserases are emerging as important epigenetic regulators of prokaryotic virulence factor and surface antigen expression12,13,14.

One such phase variable type III DNA methyltransferase of H. pylori is encoded in the prototypical genome strains J99 and 26695 by jhp1411 and hp1522, respectively; we refer to these, and the homotypic loci from all H. pylori strains, as modH 11. Phase variable regulation of modH is mediated by random alteration in the length of a guanosine (poly-G) repeat tract located 104 bp downstream of the gene region encoding the ModH DNA recognition domain (DRD). Poly-G tract length variation results in translation of either a full-length functional ModH enzyme (“ON”), or a truncated, inactive protein (“OFF”). The modH gene shows interstrain sequence diversity of the DRD region with 19 allelic types now identified (types modH1 – modH19)11,15. The prototypical strains J99 and 26695 carry alleles modH1 (jhp1411) and modH2 (hp1522), respectively, with the latter recently found to be inactive in 2669516. The first H. pylori ModH phasevarion to be examined was modH5 (hpp12_1497), carried by H. pylori strain P1211. In that study, modH5 was identified as one of the most prevalent among the 17 modH alleles identified at the time, and was carried by ~15% of isolates examined. ON-phase of P12 modH5 was shown to positively regulate the expression of motility-associated genes flaA, flgE and hpp12_0904, and negatively regulate the expression of motility-associated gene hpp12_0255 and outer membrane colonization factor gene hopG 17,18. More recently, the ModH1 phasevarion of H. pylori strain J99 has been examined and shown to also contain several motility-associated genes, including flgE 19. However, in contrast to the ModH5 phasevarion, flgE is positively regulated by the ModH1 OFF-phase. In line with these observations of ModH-mediated gene regulation, a role for ModH phase switching in H. pylori colonization has been implicated by the findings of a recent mouse model study20. Despite the predictive transcriptional evidence, the phenotypic role of ModH phase switching in H. pylori motility had not been examined. Furthermore, the DNA target recognition motif of ModH5 and the molecular mechanism by which ModH5 mediates epigenetic regulation of gene expression remained unknown.

The development of Single Molecule Real-Time (SMRT) sequencing enables both genomic and epigenomic information to be derived from bacterial DNA21,22 and has been used to characterize the methylomes of several pathogenic bacteria including Escherichia coli 21, Moraxella catarrhalis 7, H. pylori 16,19,23,24, Campylobacter coli 25, Neisseria menigitidis 26, non-typeable Haemophilus influenzae 6 and Mycobacterium tuberculosis complex species27. In particular, the data obtained have provided important insights into the activities and target DNA recognition motifs of numerous bacterial DNA methyltransferases. Here we report on identification of the target DNA recognition motif of H. pylori ModH5 methyltransferase using SMRT sequencing. This, together with findings from phenotypic and promoter analyses, provided novel insight into the mechanism by which ModH5 epigenetically controls the expression of virulence genes important for H. pylori colonization and survival.

Results

SMRT methylome characterization of H. pylori strain P12 identifies 5′-Gm6ACC-3′ as the methylation target site of ModH5

Extensive genetic diversity of the modH DNA recognition domain strongly suggests that different ModH allelic variants may methylate different target DNA motifs. To identify the ModH5 methylation target site, we performed SMRT sequencing of genomic DNA from H. pylori P12 wild-type modH5 ON, modH5 OFF11 and the ΔmodH5 deletion mutant11 strains (Table 1). The methylated bases, i.e. N6-methyladenine (m6A), N4-methylcytosine (m4C), or C5-methylcytosine (m5C), in the H. pylori P12 genome were identified by their IPD ratio; they were then aligned and clustered to identify the motif that constituted the recognition sequence for the active ModH5 methyltransferase in strain P12 (Supplementary Datafile S1). First, the results obtained from the methylome analysis on P12 wild-type (wt) not only agreed with the previously published methylome data for P1224, but also revealed an additional novel methylation target sequence, 5′-GAm6AGA-3′ whose cognate DNA methyltransferase remained unidentified (Table 1). Second, comparison of the methylome of wild-type P12 (modH5 ON) to those of modH5 OFF and ΔmodH5 isogenic mutants indicated that the ModH5 methyltransferase was responsible for the N6-adenosine methylation in the sequence 5′-Gm6ACC-3′.

Table 1 SMRT methylome analysis of the H. pylori P12 modH5 ON, modH5 OFF and ΔmodH5 strains.
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Interestingly, our SMRT data indicated that ~6% of 5′-GACC-3′ sites in the modH5 OFF and the ΔmodH5 deletion mutant strains were methylated (Table 1). A significant proportion of these Gm6ACC sites (4%) were found to overlap the target sites of other methyltransferases, namely GNGRGm6A or TCNNGm6A. The remaining ~2% of Gm6ACC sites in the mutants were called as methylated according to the QV score cut-off of 30, but had significantly low IPD ratios/QV scores compared to scores of other target sites in the same strain (e.g. GNGRGA) and GACC sites in P12 wt (Supplementary Fig. S1). Thus, we do not rule out the possibility that these latter Gm6ACC sites might be false positives.

GACC sites are underrepresented in the H. pylori genome

The P12 genome contains 2580 GACC sites on the genome and 24 sites on plasmid pHPP12, equating to frequencies of 0.77 sites/kb ssDNA and 1.17 sites/kb ssDNA, respectively. The frequency of GACC sites on the genome was markedly less than the number of sites predicted by the P12 genome GC content of 38.8% (Table 2), indicating a bias against GACC carriage. Identification of tetranucleotide relative abundance extremes, i.e. significant over- or under-representation as described by Karlin et al.28, among all possible 4-nucleotide sequences within the P12 genome confirmed a significant bias against GACC carriage. The relative abundance (τwxyz-values) of GACC and similar tetranucleotide sequences are shown in Fig. 1. Notably, this bias was conserved in the genomes of all H. pylori strains examined regardless of the modH type carried (Fig. 1a). In contrast, plasmid DNA from the same selection of H. pylori strains did not show a bias against GACC carriage, and instead showed substantial interstrain variation in tetranucleotide skewing. For example, a significant overrepresentation of GACC was observed in the P12 plasmid pHPP12 (Fig. 1b), despite pHPP12 having a lower overall GC content (35%) than the P12 genome. Tetranucleotide composition was also examined in the genomes of various non-pylori Helicobacter species but the tetranucleotide skewing was different between each species examined, as well as to that observed in H. pylori genomes, and did not include GACC underrepresentation (Supplementary Fig. S2a). In contrast, similar analysis of other naturally competent bacterial species indicated that some other bacterial genera did have conserved tetranucleotide skewing, including Campylobacter species also showing a bias against GACC in their genome (Supplementary Fig. S2b). These observations suggest that there is significant selective pressure to restrict the occurrence of GACC in the H. pylori chromosome, and that this selection is preserved in H. pylori strains independently of whether they carry the modH5 allele. Moreover, this bias is not observed in other Helicobacter species, but can occur in other Epsilonproteobacteria.

Table 2 Distribution of GACC sites throughout the P12 chromosome.
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Figure 1
figure 1

Over- and under-representation of GACC-related tetranucleotide motifs in Helicobacter species and naturally competent non-Helicobacter species. Tetranucleotide representation in: (a) H. pylori chromosomal DNA tetranucleotide representation, modH type in brackets; and (b) H. pylori plasmid DNA, plasmid size and modH type in brackets. Tetranucleotide extremes were examined using Signature (Institute of Bioinformatics, University of Georgia) to determine Karlin’s tau (τwxyz) values whereby <0.72 (dashed line) or >1.28 (dotted line) indicate significantly underrepresented or overrepresented tetranucleotide motifs, respectively.

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The ModH5 recognition site GACC is overrepresented in motility and outer membrane protein genes

The ModH5 GACC target sequence was widely distributed throughout the genome and equivalently present on each strand (Fig. 2a and Table 2). The proportion of GACC sites in intergenic regions (5.7%) was significantly less than expected given that 8.2% of the P12 genome is intergenic (Chi square P < 0.0001; odds ratio 0.67, 95% CI 0.57 to 0.79). Close examination of the position of GACC sites with respect to all individual gene loci showed that GACC sites were commonly found both proximal to and within coding regions, with 52% of the annotated P12 genes having one or more GACC site within the 500 bp upstream of the start codon (Fig. 2b), and 68% of genes containing at least one GACC site within the coding region (Fig. 2c).

Figure 2
figure 2

GACC distribution on H. pylori P12 genome. (a) Forward strand (1340 GACC sites) and reverse strand (1240 GACC sites) of the P12 genome. From outside track: turquoise-ORFs; GACC frequency, orange–high, green–low; %GC content, pink–high, purple–low. Red bars denote areas of interest in the P12 genome (clockwise): comB, including type IV secretion system (TFSS) 2; PZ1–plasticity zone 1, including TFSS4; cagPAI–cag PAI pathogenicity island, including TFSS1; PZ2–plasticity zone 2; PZ3–plasticity zone 3, including TFSS3. (b) Distribution of the number of GACC sites in 500 bp region upstream of all P12 genes. (c) Distribution of the number of GACC sites in all P12 genes. (d) There was a significant positive correlation between the number of GACC sites within a gene and the length of the gene (Spearman’s correlation).

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Although there was a direct correlation between gene size and number of GACC sites within the coding regions (Fig. 2d), a subset of genes showed GACC frequency above that expected from this correlation with gene size. Due to the low prevalence of GACC in the P12 genome, a comparison of individual gene size against its GACC frequency (GACC sites per kb) indicated that genes <500 bp in length had dramatically exaggerated GACC frequency, which is likely a statistical artefact due to the low frequency of GACC throughout the genome (Supplementary Fig. S3a). After excluding this subset of genes (i.e. <500 bp in length), the remaining 902 genes were shown to carry a median of 1.66 GACC sites/kb dsDNA (interquartile range 1.15–2.46) (Supplementary Fig. S3b). Consequently, genes with a GACC frequency higher than the upper interquartile range of 2.46 GACC sites/kb dsDNA (226 genes) were considered to have significant GACC overrepresentation, of which genes with 6 or more GACC sites are listed in Table 3.

Table 3 List of the top 31 GACC-hypermethylated genes. aDuplicated ORFs with 100% nucleotide identity share the same rank. bBlue-shaded rows denote outer membrane and virulence proteins. cPink-shaded rows denote motility-associated genes. dBolded text denote genes previously identified to be regulated by modH5 ON/OFF status11. Genes are ranked firstly according to the number of GACC sites within each ORF (≥6), and secondly according to the number of GACC sites/kb for each ORF. Only >500 bp genes with >2.46 GACC sites/kb were considered.
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Notably predominant among these top 31 genes are two functional groups that are critical for H. pylori pathogenesis, namely motility/chemotaxis-associated proteins (seven genes) and adhesion/cytotoxicity proteins (eight genes). Amongst the latter group, the genes encoding HopZ, VacA and Cagβ/VirD4 are of particular interest with respect to H. pylori pathogenesis. Of the five adhesin genes, three (hopZ, sabB and sabB_2) have two other known phase variable modes of regulation i.e. translational regulation via dinucleotide repeats in the signal sequence and transcriptional regulation via a homopolymeric T-tract in the promoter region29,30.

H. pylori motility is regulated by modH5 phase switching

Motility is crucial for H. pylori colonization of the gastric mucosa31,32. We previously reported that four of the five genes identified by transcriptional microarray as members of the ModH5 phasevarion of H. pylori strain P12 are motility-associated11. These genes were flaA (hpp12_0609), flgE-1 (hpp12_0870), fliK (hpp12_0904) and hpp12_0255, which respectively encode the major flagellin subunit A, flagella hook protein, flagella hook-length control protein, and a homolog of the Salmonella flagella-associated chaperone FliJ that has been shown to be essential for full motility and adhesion in H. pylori 17. In this present study, we bioinformatically identified nine motility genes as having GACC overrepresentation, of which seven were in genes that carry GACC at very high frequency (Table 3). In particular, flaA (Fig. 3a) and flgE-1 (Fig. 3b) carried a very high frequency of GACC sites compared to the remainder of the P12 genome and were among the top 10 genes showing GACC overrepresentation (Table 3). The distribution of GACC sites in the remaining motility genes included in Table 3 are shown in Supplementary Fig. S4.

Figure 3
figure 3

ModH5 ON/OFF state differentially modulates H. pylori P12 motility. GACC ModH5-target sites are overrepresented in essential motility genes flaA (a) and flgE-1 (b), which have both previously been shown to be transcriptionally modulated by modH5 ON/OFF state. The schematics show the known promoter features (filled boxes) and open reading frames (filled arrow) of the motility genes, and their flanking genes (open arrows). (c) Representative motility images of modH5 ON (P12 wt), modH5 OFF and ΔmodH5 strains stabbed into soft agar; images captured at 5 days post-inoculation; the addition of tetrazolium chloride to the soft agar allowed visualisation of the distance travelled (outer red ring) over time; scale bar = 5 mm. (d) Comparative motility of modH5 ON (P12 wt), modH5 OFF and ΔmodH5 strains; bars denote mean ± SD (each symbol represents the mean of technical replicates from an individual experiment; P12 wt and P12ΔmodH5, N = 4 independent experiments; P12 modH5 OFF, N = 3 independent experiments); P-values determined by two-way ANOVA, *P < 0.05, ****P < 0.0001 denote significant enhancement in motility of P12 wt compared to isogenic OFF strains; significant migration of each strain between d3 and d5 indicated beneath each d5 dot plot.

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Our bioinformatics analysis, together with the previous transcriptional ModH5 phasevarion analysis11, suggested that ModH may be a novel regulator of H. pylori motility. We therefore hypothesised that although transcription of individual motility genes was only moderately affected by modH5 ON/OFF state, the combined impact from differential expression of multiple motility-associated genes would have a measurable effect on H. pylori motility phenotype(s). To test this hypothesis, we compared the motility of wild-type P12 modH5 ON strain with that of the P12 modH5 OFF and P12∆modH5 strains by stab-inoculating the strains onto motility agar plates (Fig. 3c). P12 wt and the mutant strains showed significant migration through the soft agar by 5 days post-inoculation (dpi) compared to 3 dpi (Fig. 3d) indicating that all three strains were motile. However, motility of P12 wt modH5 ON was significantly enhanced compared to the mutant strains at both 3 dpi (~50% increase, P < 0.05) and 5 dpi (~2-fold increase, P < 0.0001) (Fig. 3d). These findings demonstrate that ModH5 plays a key role in modulating H. pylori motility.

Given the differential expression of genes encoding the flagella structural components flagellin A (flaA) and the hook protein (flgE-1), we also visually assessed flagella of the wt and mutant strains by transmission electron microscopy (Supplementary Fig. S5). P12 wt had on average three times as many flagella per bacterial cell than the two mutant strains (Fig. 4a and b), with ~30% of modH5-OFF or ΔmodH5 cells being aflagellated (Supplementary Fig. S5d). This substantial difference may be sufficient to account for the observed enhanced motility of the modH5-ON strain. We also detected minor differences in the length (Fig. 4c) and width (Fig. 4d) of flagella on the different strains, however these differences did not appear to correlate with modH5 ON/OFF-status.

Figure 4
figure 4

ModH5 ON/OFF state differentially modulates H. pylori P12 flagella number. (a) Paraformaldehyde-fixed, broth-cultured H. pylori modH5 ON (P12 wt), modH5 OFF and ΔmodH5 strains were adsorbed onto formvar copper grids, negative stained with ammonium molybdate and imaged by transmission electron microscopy; 3 representative images shown of each strain (scale bar = 1 μm). Individual bacterial cells were assessed using Fiji ImageJ software for (b) number of flagella per cell (magnification 8000x), (c) flagella length (magnification 8000x), and (d) flagella width (magnification 50,000x). P-values were determined by Kruskal-Wallis test with Dunn’s multiple comparison post-test; *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001; all other comparisons not significantly different. Sample sizes for each group shown in parentheses.

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GACC sites flanking the flaA promoter are sufficient for ModH5-dependent modulation of promoter function

Both flaA and flgE-1 had Gm6ACC sites upstream of, and within, the ORF. In particular, the GACC methylation profile of flaA included 8 Gm6ACC sites throughout the flaA gene, all on the template strand and starting 14 bp into the ORF, and an additional Gm6ACC site on the coding strand 507 bp upstream of the flaA transcriptional start site (Fig. 3a). The mechanism(s) by which upstream and/or intragenic ModH target motifs contribute to phase variable H. pylori epigenetics may provide important insight into H. pylori pathogenesis. We were therefore interested in using flaA as a model system to identify specific methylation sites involved in ModH5-mediated gene regulation.

We constructed a flaA expression reporter plasmid by cloning 1.1 kb of the P12 genome containing the flaA promoter into the promoterless green fluorescent protein (GFP)-reporter vector pTM11733. The resultant flaA-gfp transcriptional fusion plasmid is designated pTM117-flaA. Previous reporter studies examining stimuli-mediated regulation of the native flaA promoter typically included not only the flaA upstream sequence, including the transcriptional start/σ28/−10/−35 promoter region (nt 642,138 to 642,188), but also a proportion of the flaA coding region in the upstream sequence of the reporter construct to drive reporter gene expression34,35,36. Therefore, taking into account the possibility that elements within the flaA coding region might somehow be involved in flaA promoter regulation, we included both the GACC located upstream of flaA ORF (GACC1) and the first internal GACC site adjacent to the start codon (GACC2), in the promoter region of pTM117-flaA to drive gfp expression (Fig. 5a). Transformation of P12 with this construct was repeatedly unsuccessful, which is in contrast to its ready acceptance of linear DNA but is typical of this strain for circular plasmid DNA. Therefore this construct was used to transform H. pylori strain 7.13 that also carries the modH5 allele11, but is more readily transformed by plasmid DNA than most H. pylori strains. Unlike the P12 modH5 that contains a short, relatively low-frequency switching modH5 G10-tract, quantitative sequence analysis of the 7.13 modH5 polyG-tract length using specific fluorescent-tagged primers showed that the parent 7.13 wt strain was a mixed population of modH5 ON (G13) and OFF (G11, G12 & G14) at 43% versus 57%, respectively. This diversity in G-tract length validated the inherent capability of the modH5 allele in 7.13 to phase vary at high frequency under the experimental conditions used.

Figure 5
figure 5

ModH5-mediated methylation of the flaA promoter region modulates downstream gene expression. (a) pTM117-flaA reporter construct design. DNA containing GACC sites upstream of, and at the start of, the P12 flaA ORF was inserted upstream of a promoterless gfpmut3 gene within plasmid pTM11733. (b) Transformation of H. pylori modH5 strain 7.13 resulted in both GFP-fluorescent and non-fluorescent kanamycin-resistant transformants as measured by flow cytometric analysis of transformants (green peak) compared to parental 7.13 (grey peak); x-axis denotes GFP fluorescence intensity and y-axis denotes number of cells. Inset chromatograms of the polyG-tract in modH5 gene of each transformant showing the GFP-fluorescent clones were modH5-ON and the non-fluorescent clones were modH5-OFF. (c) gfp mRNA levels in GFP-fluorescent versus non-fluorescent transformants as determined by qPCR using 16S-specific and gfp-specific qPCR of random primed cDNA generated from bacterial RNA. Three independent transformants were assessed per fluorescence phenotype; each symbol type (circle, triangle or square) represents an individual clone; open symbol = 16S qRT-PCR, filled symbol = gfp qRT-PCR; each point represents mean (±SD) of technical triplicates.

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Transformation of 7.13wt by plasmid pTM117-flaA resulted in a mixture of kanamycin-resistant (KmR) transformants that were either GFP-fluorescent or non-fluorescent. Transformants were randomly selected for gfp expression analysis by flow cytometry, and sequence analysis across the modH5 polyG tract (Fig. 5b). This analysis showed a direct correlation between gfp expression and ModH5 function in that GFP-fluorescent and non-fluorescent transformants had in-frame and out-of-frame modH5 G-tracts, respectively. Quantitative analysis of gfp mRNA level indicated a dramatic defect in gfp transcription by the modH-OFF transformants compared that in the modH-ON transformants (Fig. 5c). In contrast, 16S rRNA expression was indistinguishable between the different strains. Together these results suggest that flaA promoter activity can be modulated by ModH5 phase variation, likely via altered methylation of the two GACC sites in the promoter construct.

GACC1 is essential for ModH5-dependent flaA promoter-regulation

In order to assess the contribution of specific Gm6ACC sites to flaA promoter function, we modified the methylated nucleotide in GACC1 of pTM117-flaA from A to C (i.e. GCCC, a sequence no longer recognised by ModH5). The resultant construct, designated pTM117-flaA-GCCC1, was introduced in parallel with the wt promoter construct pTM117-flaA into H. pylori 7.13 wt. Interestingly, the mutant flaA promoter construct produced a mixture of GFP-fluorescent and non-fluorescent transformants in a similar manner to the wt flaA promoter construct (Fig. 6a). However, whilst modH5 G-tract sequencing of 30 randomly selected pTM117-flaA transformants revealed a direct correlation between gfp expression and modH5 ON status (P < 0.0001, Fisher’s exact test) (Fig. 6b), sequencing of 26 pTM117-flaA-GCCC1 transformants indicated that this correlation was lost as a result of GACC1 to GCCC1 substitution (Fig. 6b). These observations suggest that the upstream ModH5 target sequence plays a direct and pivotal role in epigenetic regulation of flaA promoter activity.

Figure 6
figure 6

ModH5-mediated methylation of the flaA promoter region at site GACC1 modulates downstream gene expression. (a) pTM117-flaA reporter construct carrying either GACC1 (wt promoter) or GCCC1 (A > C synonymous substitution mutant) was used to transform H. pylori modH5 strain 7.13 wt; “Epi” - total population of kanamycin-resistant transformants imaged by epi-luminescence (colonies false coloured red in ImageJ); “GFP” - fluorescent transformants imaged using a GFP-specific filter (colonies false coloured green in ImageJ); “Overlay” shows proportion of GFP-fluorescent transformants (yellow/green) to non-fluorescent transformants (red). (b) Sequencing of the modH5 G-tract in GFP-fluorescent (GFP +ve) and non-fluorescent (GFP −ve) transformants carrying pTM117-flaA with GACC1 versus GCCC1 showed that the correlation between ModH5 activity and P12 flaA promoter function was uncoupled upon loss of the upstream ModH5 methylation site (GACC1). P-values were determined using Fisher’s exact test; ****P < 0.0001, NS = not signficant.

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Discussion

H. pylori strains possess multiple methyltransferases, including orphan methyltransferases, but the biological role of the majority of these methyltransferases remained unknown16,37. We have previously reported that the activity of the H. pylori phase variably-regulated DNA methyltransferase ModH5 results in the coordinated regulation of multiple genes. This ModH5-controlled phase variable regulon, or phasevarion, includes various motility-associated genes11. These primary findings were recently bolstered by a subsequent characterisation of the H. pylori J99 ModH1 phasevarion, which was shown to also include motility-associated genes19. Despite this, the mechanism(s) by which random ModH5-phase switching controls gene expression remained uninvestigated. To elucidate the molecular basis of ModH5-associated gene regulation, a crucial prerequisite is to identify the ModH5 methylation target site. In this study, we used whole-genome SMRT sequencing to confirm that ModH5 is a functional N6-methyladenosine methyltransferase, and to identify its methylated target sequence as 5′-Gm6ACC-3′. We also demonstrated that P12 motility is modulated by ModH5 activity, and that modH5 ON phase correlates with enhanced P12 flaA promoter activity compared to modH OFF phase. To our knowledge, this is the first reported phenotypic evidence of H. pylori epigenetic motility regulation. These findings, together with previous transcriptional analyses on the ModH5 and ModH1 phasevarions, strongly suggest an important role for ModH phasevarions in virulence gene regulation and H. pylori pathogenesis.

The two ModH enzymes characterised to date, ModH5 and ModH1, methylate at target sequences 5′-Gm6ACC-3′ (this study) and 5′-GWCm6AY-3′24, respectively. These target sequences are both unique to H. pylori. Interestingly, GACC sites are significantly underrepresented in the chromosomal DNA but not in the resident plasmids of various H. pylori strains nor the genomes of other Helicobacter species. Underrepresentation of restriction-modification target sites has not previously been reported for a type III restriction-modification target sequence, although it is commonly associated with type II restriction-modification systems, particularly those recognising palindromic targets38. Moreover, conserved avoidance of a restriction-modification target sequence within a bacterial genome seems to be more common among anciently acquired restriction-modification systems compared to newly acquired systems39. The conservation of this bias against GACC in the H. pylori genome would therefore suggest a long-term presence of this system in H. pylori strains, and is in keeping with the modH5 allele being one of the most prevalent types among the strains examined previously11. Accordingly, we hypothesize that the bias against GACC sites is due to long standing selective pressure that favours strategic positioning of ModH5 target sites throughout the genome, further highlighting a role for ModH5 in H. pylori gene regulation.

Epigenetic regulation in a large number of bacteria including E. coli, Salmonella and Caulobacter have been well described and reveal a variety of mechanisms for mediating gene regulation40. A recurrent theme among these mechanisms is that DNA methylation can alter interactions between regulatory proteins and DNA-binding sites, directly regulating transcription41. In contrast, very little was known about the mechanism of epigenetic gene regulation in H. pylori. In this study, the ModH5 methylation motif GACC was found to be significantly underrepresented in the intergenic regions compared to the coding genome of P12, suggesting that upstream GACC sites are likely to be under positive selective pressure. For flaA, whose expression is increased in modH5 ON11, one GACC site is located ~495 bp upstream (GACC1) and another site 73 bp downstream (GACC2) of well-defined essential promoter elements34. The results of our reporter assay argue that these two GACC sites flanking the promoter are sufficient for transcriptional regulation by modH5 ON/OFF phasing, and that the distal GACC1 site is required for ModH5-mediated flaA promoter regulation. More specfically, our data indicates that flaA promoter function becomes uncoupled from ModH5 in the absence of GACC1 methylation, and control reverts to ModH5-independent regulators of flagella production. Whilst the precise mechanism by which ModH5 methylation of flaA promoter GACC site(s) results in gene activation remains to be elucidated, our analysis of GACC distribution also indicated that some other target genes of ModH5 do not contain GACC sites in close enough proximity to the upstream regulatory region to directly impact upon promoter function. For example, the closest upstream GACC of fliK (hpp12_0904) is 1141 bp upstream of the ribosome binding site. This argues that the mechanism(s) by which ModH5 regulates gene expression might vary from one gene to another. Meanwhile, the promoter regions of some ModH5 phasevarion genes are either unknown (e.g. fliK) or sigma factor 54-driven promoters which have distant enhancer binding sites42 (e.g. flgE). In these cases, the functional distance of GACC sites from such promoters remains speculative. Future investigation into the molecular basis of gene regulation by ModH5 for the various other target genes is warranted to shed light on the diversity of mechanisms involved.

We have also noted a comparative abundance of GACC sites within the coding regions of numerous virulence genes. A similar phenomenon has been described for ModH1 recognition sites in J9919. There is recent evidence of gene regulation mediated by methylation of ORF-encoded target sites by the VchM methyltransferase of Vibrio cholera 43. Among the large number of VchM-regulated genes, there was a significant correlation between the number of target sites within the coding region of a gene and enhanced expression level of the gene, particularly for genes containing more than 4 target motifs. How these sites that are located within coding regions influence gene expression is as yet unknown. However it is well reported that eukaryotic DNA methylation within an open reading frame can influence splicing of the resultant mRNA, thereby providing evidence that DNA methylation may influence not only interactions between DNA and gene regulatory proteins, but also RNA synthesis and/or post-transcriptional processing events44.

Flagellar motility is essential for gastric colonization and sub-organ localization within the stomach45. Motility consumes vast amounts of energy and therefore needs to be tightly regulated transcriptionally. The mechanisms involved in motility regulation are highly complex and not fully understood. The H. pylori flagellum is comprised of three main structural components; the filament composed of flagellins FlaA (the major component) and FlaB (a minor component), the hook-associated proteins FlgK and FlgL, and the hook protein FlgE. Our observation in this study that wild-type P12 (ON) has enhanced motility compared to the P12 modH5 OFF strain is in line with our previous findings that motility-essential genes flaA and flgE are increased in expression when modH5 is ON11, highlighting the novel role of ModH5 in motility regulation. However, how does the role of ModH5 in motility regulation reconcile with the previous finding that phase variable regulation of motility is mediated in some strains by slippage of a homopolymeric C8-tract within the motility-associated gene fliP 46? Interestingly, fliP expression in H. pylori P12 and J99 is fixed “ON” via the alternate CCCCACCC sequence. It is thus possible that phase variable regulation of motility in strain P12 occurs not via fliP phase switching but rather through ModH5 phase variable epigenetic regulation of flaA promoter activity; this might hold true also for other strains such as J99. Apart from directly regulating flaA promoter activity, we postulate that ModH5 could also modulate flaA expression indirectly. Expression of flaA, which is driven from a sigma factor 28 -controlled promoter, is dependent on environmental signals and also on regulatory systems that ensure the sigma factor 54 -controlled flagella hook is assembled in preparation for the hook-filament transition47,48. One of the important regulators of flaA, FliK, helps to release sigma factor 28 from the anti-sigma factor 28 factor FlgM in response to environmental cues, thereby making sigma factor 28 factor available for flaA expression49. Notably, fliK, like flaA and flgE, is also downregulated in the absence of ModH5-mediated methylation11, suggesting that ModH5 might also be able to modulate flaA expression indirectly through regulation of fliK expression. However, given that reduced fliK expression typically results in flgE over-expression50, we hypothesize that phase variable epigenetic modulation of flaA, flgE and fliK expression might act as an additional ‘rheostat’ to fine tune positively and/or negatively the expression of various motility genes and hence their roles in H. pylori colonization, nutrient acquisition and host adaptation.

The recent ‘epigenetics-driven adaptive evolution’ hypothesis suggests that diverse methylomes rather than diverse genome sequences are ideal targets for natural selection51, and the inherent genetic mobility of H. pylori mod DNA recognition domains provides a novel mechanism for rapid diversification52. In line with these notions, we propose that a combination of ModH ON-OFF phase switching, variable DNA-methylation specificity and differing phasevarion composition would generate tremendous diversity crucial for H. pylori to adapt to the highly variable and complex host microenvironment whilst evading host immune defense.

Taken together, the findings of this and other recent studies on H. pylori methylomes highlight the emerging importance of DNA methyltransferases as a important epigenetic regulator of virulence gene expression and a critical driver of bacterial evolution and adaptation. This study has provided an important basis for further investigation into the underlying molecular mechanisms, knowledge of which is likely to revolutionize our understanding of bacterial epigenetics and its role in H. pylori pathogenesis.

Methods

Strains and growth culture conditions

H. pylori strains were routinely grown from glycerol stocks for 2 days on GC agar (Oxoid, Basingstoke, UK) plates supplemented with 10% (v/v) horse serum (Invitrogen Corp, Carlsbad, CA), vitamin mix and antibiotics (nystatin, 20 μg/ml; trimethoprim, 2.5 μg/ml; vancomycin, 10 μg/ml) in a microaerobic atmosphere as described previously11. Plates for cultivation of mutant strains were further supplemented with chloramphenicol (4 μg/ml for routine culture, 10 μg/ml for selection of transformants). H. pylori strains used in this study were P12 wild-type (also designated modH5 ON; in-frame G10 tract; phenotype modH ON), P12∆modH::cat (also designated ∆modH5; replacement of modH DRD with cat cassette; phenotype modH OFF)11, P12 modHOFF::cat (also designated modH5 OFF; in-frame G10-tract substituted to out-of-frame G6AG4, and region after premature stop codon replaced with a cat cassette; phenotype modH OFF)11, and 7.13 wild-type showing heterogeneous modH G-tract lengths.

Analysis of modH5 repeat tract

The length of the poly-G repeat tract was determined by Sanger sequencing, using primer pair ModHF_repeat (5′-ATGCCGTGTTAGAGAGTAATAAGAGCGA-3′) and ModHR_repeat (5′-TCTAACTGGACGAGAATGAAGCG-3′) to amplify the repeat regions of modH5. 6-carboxyfluoroscein-tagged ModHF_repeat primer was used together with unmodified ModHR_repeat to quantitate proportions of different poly G-tract lengths in parental H. pylori strains.

SMRT sequencing

Genomic DNA was extracted from plate-cultured H. pylori strains using the QIAGEN DNeasy blood and tissue genomic DNA kit as per the manufacturer’s instructions. SMRTbell libraries were prepared as previously described53 according to the manufacturer’s instructions (PacBio, CA, USA). Briefly, genomic DNA was sheared to an average length of approximately 10 kb using g-TUBEs (Covaris; Woburn, MA, USA), treated with DNA damage repair mix, end-repaired and ligated to hairpin adapters. Incompletely formed SMRTbell templates were digested using Exonuclease III (NEB) and Exonuclease VII (Affymetrix; Cleveland, OH, USA). Sequencing was carried out on the PacBio RS II (Menlo Park, CA, USA) using standard protocols for long-insert libraries.

Bioinformatic and statistical analysis

Reads were mapped against the P12 genome and plasmid sequences (accession numbers CP001217 and CP001218, respectively). The ModH5 methylation recognition site was identified using the Pacific Biosciences’ SMRTPortal analysis platform (v. 1.3.1) as described previously54, and its locations relative to genome features analysed using Artemis55 and in-house scripts written in Perl and Python. Circular genome figures were created using DNAPlotter56 using data derived from the Prokka annotation and SMRT methylome. Comparative analysis of tetranucleotide extremes in H. pylori genomes was performed using the Signature server (Institute of Bioinformatics, University of Georgia; http://www.cmbl.uga.edu/software/signature.html) to determine Karlin’s tau (τwxyz) values whereby values less than 0.72 or greater than 1.28 indicate significantly underrepresented or overrepresented tetranucleotide motifs, respectively. Statisitcal analysis of GACC prevalence and motility was performed using GraphPad Prism software (v6.0 h).

Motility assay

Approximately 4 × 106 CFU of broth-grown H. pylori P12 wild-type or isogenic modH5 mutant strains was stabbed in 5 µl volumes into triplicate soft agar motility plates (20 ml agar dispensed per plate; Brucella broth (BD Biosciences), 7% (v/v) fetal bovine serum (Gibco), 0.4% (w/v) agar (No. 1, Oxoid) and 40 μg/ml metabolic activity indicator triphenyl tetrazolium chloride (Sigma, UK)). Plates were incubated at 37 °C under microaerobic conditions and bacterial motility was assessed by measuring two perpendicular diameters of metabolically active bacteria across each stab after 3 and 5 days growth. For each experiment, averaged diameters of each strain were converted to area (π(d/2)2) of bacterial migration, and data from independent experiments were combined for statistical analysis.

Transmission electron microscopy

For transmission electron microscopy analysis, 1 mL of cells from Brucella broth-grown wild type and mutant strains was pelleted by centrifugation (3 mins at 8,000 rpm), and resuspended in 1% (w/v) neutral buffered paraformaldehyde (30 mins, room temperature). Fixed cells were washed twice with PBS (pH 7.2) and adsorbed onto Formvar, carbon-coated Cu grids (10 μl per grid). Grids were negatively stained with 0.3% (w/v) ammonium molybdate (15 seconds), air dried, and desiccated until imaging under a Phillips CM120 electron microscope at 80 kV.

Creation of flaA-gfp promoter fusion plasmid constructs

The transcriptional fusion of flaA (HPP12_0609) to the promoterless gfpmut3 gene in pTM117 (accession number EF540942)33 was constructed by amplification of the promoter region of the flaA gene from P12 genomic DNA using primers FlaA_SacII_F (5′-TCCccgcggGAGCTAAATGCTTGGATATATCCAGCAAT-3′) and FlaA_BamHI_R (5′-CGCggatccCATTTTGAGTGAGTGCGGATTGC-3′) to generate a 1136-bp amplicon. This product was cloned into pGEM-T Easy to generate pGEMflaA, and confirmed by sequencing. The flaA fragment was excised by SacII/BamHI digestion and cloned into the same sites of the transcriptional fusion vector pTM117 to create pTM117-flaA. The pTM117-flaA plasmid was moved into H. pylori strain 7.13 wild-type by natural transformation, and transformants were selected on GC plates containing 10 μg/ml kanamycin. Transformants were graded as GFP-fluorescent or non-fluorescent by their fluorescent intensity detected using LAS-3000 Intelligent Darkbox (FujiFilm) in comparison to H. pylori 7.13 wild-type. Sequence integrity was confirmed by Sanger sequencing for pTM117-flaA plasmid recovered from three GFP-fluorescent and three non-fluorescent transformants; Southern hybridisation analysis of whole genomic DNA confirmed that the flaA-gfpmut3 fusion was retained in the plasmid and had not integrated into the chromosome of 7.13 transformants.

GFP expression reporter assays

GFP expression level in H. pylori 7.13(pTM117-flaA) GFP-fluorescent and non-fluorescent transformants was measured by flow cytometry. Strains were grown overnight in liquid culture; 1.5 ml of each culture was pelleted resuspended in 1 ml 4% (w/v) paraformaldehyde in phosphate-buffered saline (PBS) for 20 mins, then resuspended in 1 ml PBS and passed through a 35 μm cell strainer to remove any bacterial clumps or debris. The samples were then analyzed using a BD LSR-II flow cytometer to collect 100,000 events. Flow cytometry data was analyzed using Flowing software (Cell Imaging Core, Turku Institute for Biotechnology, Finland).

Quantitative RT-PCR

Overnight Brain Heart Infusion broth cultures (10 ml) of GFP-fluorescent and non-fluorescent 7.13(pTM117-flaA) transformants were pelleted, resuspended in 100 μl TE buffer (10 mM Tris/1 mM EDTA [pH 8]) supplemented with 1 mg/ml lysozyme, incubated for 20 mins, 37 °C, before adding 350 μl RLY cell lysis buffer (ISOLATE II RNA mini kit, Bioline) supplemented with 10 mM dithiothreitol, and continuing RNA purification according to the kit protocol for “purifying total RNA from cultured cells and tissue”. RNA concentrations were estimated by Nanodrop (Thermo Fisher) and 500 ng RNA was used for cDNA production using the Superscript III first strand synthesis system with random primers (Thermo Fisher) according to the kit protocol. gfp mRNA levels were assessed by qPCR using FastStart Universal SYBR Green Master mix (Roche) with gene-specific primers for gfp (gfp_qPCR_F 5′-TGTTCCATGGCCAACACTTG-3′ and gfp_qPCR_R 5′-GCACGTGTCTTGTAGTTCCC-3′) and 16 S rRNA (Hp547f 5′-CTTAACCATAGAACTGCATTTGAAACTAC-3′ and Hp665r 5′-GGTCGCCTTCGCAATGAGTA-3′57). Quantitative PCRs were prepared in triplicate and individual 25 μl reactions contained 0.4 mM primer pair and 2 μl cDNA (≈50 ng RNA) or nuclease-free H2O (no-template control). PCR cycling conditions were: 1 cycle (95 °C for 10 min); 40 cycles (95 °C for 15 s, 60 °C for 60 s); melting curve from 65 °C–95 °C, 5 s per 1 °C. Output qPCR data was assembled into amplicon groups and analysed using LinRegPCR (software version 2017).