Many host-adapted bacterial pathogens contain DNA methyltransferases (mod genes) that are subject to phase-variable expression (high-frequency reversible ON/OFF switching of gene expression). In Haemophilus influenzae and pathogenic Neisseria, the random switching of the modA gene, associated with a phase-variable type III restriction modification (R-M) system, controls expression of a phase-variable regulon of genes (a “phasevarion”), via differential methylation of the genome in the modA ON and OFF states. Phase-variable type III R-M systems are also found in Helicobacter pylori, suggesting that phasevarions may also exist in this key human pathogen. Phylogenetic studies on the phase-variable type III modH gene revealed that there are 17 distinct alleles in H. pylori, which differ only in their DNA recognition domain. One of the most commonly found alleles was modH5 (16% of isolates). Microarray analysis comparing the wild-type P12modH5 ON strain to a P12ΔmodH5 mutant revealed that six genes were either up- or down-regulated, and some were virulence-associated. These included flaA, which encodes a flagella protein important in motility and hopG, an outer membrane protein essential for colonization and associated with gastric cancer. This study provides the first evidence of this epigenetic mechanism of gene expression in H. pylori. Characterisation of H. pylori modH phasevarions to define stable immunological targets will be essential for vaccine development and may also contribute to understanding H. pylori pathogenesis.
Citation: Srikhanta YN, Gorrell RJ, Steen JA, Gawthorne JA, Kwok T, Grimmond SM, et al. (2011) Phasevarion Mediated Epigenetic Gene Regulation in Helicobacter pylori. PLoS ONE 6(12): e27569. https://doi.org/10.1371/journal.pone.0027569
Editor: Holger Bruggemann, Aarhus University, Denmark
Received: June 3, 2011; Accepted: October 19, 2011; Published: December 5, 2011
Copyright: © 2011 Srikhanta 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.
Funding: This work was supported by an Australian National Health and Medical Research Council (NHMRC) Biomedical Research Fellowship to YNS, NHMRC Program Grant 565526 to MPJ, NHMRC Program Grant 284214 to MPJ and RRB, and NHMRC Project Grant 519704 to MPJ and SMG. 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.
The host-adapted pathogen Helicobacter pylori is the most common cause of bacterial infection worldwide ,  and is an important etiologic agent of gastritis, peptic ulcers, and gastric cancer , . Unless treated, colonization usually persists for life, indicating that H. pylori is well adapted to the gastric environment.
In order to adapt its physiology to its environment and ensure survival, H. pylori has evolved molecular mechanisms for generating genetic variation . One mechanism is phase-variation, which is the high frequency reversible on/off switching of gene expression. Phase-variation is commonly mediated by mutations in simple tandem DNA repeats in the open reading frame or promoter region of genes encoding surface expressed virulence determinants . The independent, random switching of these genes results in phenotypically diverse populations that can rapidly adapt to host environments and evasion of immune responses . While phase-variation is typically associated with genes encoding surface structures, several host-adapted bacterial pathogens, including H. pylori, have DNA methyltransferases (mod genes) associated with type III restriction modification (R-M) systems that contain simple tandem DNA repeats which have been proven to phase vary , , .
R-M systems are ubiquitous in bacteria and confer protection to the bacterial host against invasion by foreign DNA . R-M systems are classified into three groups: Types I, II or III on the basis of their subunit composition, DNA cleavage position, sequence-specificity and co-factor requirements . Type III systems are composed of a methyltransferase (modification, mod) gene and an endonuclease (restriction, res) gene, whose products form a two-subunit enzyme – Mod and Res . In Type III systems Res must form a complex with Mod to be functional , although, Mod can function independently of Res . The Mod subunit contains several conserved motifs in the N- and C-terminal regions and the central region contains the DNA-recognition domain that dictates sequence specificity .
We have recently shown that in three human pathogens (Haemophilus influenzae , Neisseria gonorrhoeae and Neisseria meningitidis ) the random switching of the modA gene controls expression of a phase-variable regulon of genes (a “phasevarion”), via differential methylation of the genome in the modA ON and OFF states. In this study we investigated the modH gene, a phase-variable DNA methytransferase of H. pylori, to determine if it plays a role in gene regulation.
Seventeen modH alleles present in H. pylori
To investigate if the modH gene associated with a type III R-M system of H. pylori behaves as a phasevarion , , we first carried out phylogenetic analysis of modH. We have previously reported that Helicobacter strains, like the pathogenic Neisseria, contain multiple phase-variable type III R-M systems . We defined one of these phase-variable type III R-M systems as modH. As with H. influenzae and the pathogenic Neisseria , , for each mod gene of H. pylori there are distinct alleles that differ only in their DNA recognition domain (; see Figure 1A). Comparison of the fully sequenced and annotated H. pylori genomes available at the time revealed that there were four distinct alleles of modH based on differences in their DNA recognition domain . The modH gene contains tracts of simple tandem guanosine repeats that mediate phase-variation of mod gene expression.
(A) Diagrammatic representation of the mod and res genes of H. pylori. The methyltransferase gene (mod) and restriction endonuclease (res) genes and the repeat region that mediates phase-variation are indicated. Type III R-M system conserved motifs are also shown: in mod, the catalytic region (DPPY), the AdoMet binding pocket (FxGxG), and the DNA recognition domain (DRD); in res, the ATP binding motif (TGxGKT), and ATP hydrolysis motif (DEPH) and the endonuclease domain. A black circle indicates the position of a nonsense mutation or frame-shift mutation in res. (B) The variable regions for each of the 17 modH alleles in the multiple sequence alignment were aligned in ClustalW and visualised with JalView using the overlay feature. The nucleotides are represented as vertical bars colored according to consensus identity (dark blue >90% identity; light blue >50% identity; white <50% identity or gap). The modH alleles were from the following H. pylori strains (listed in Table 1); modH1 BH13, modH2 1061, modH3 11637, modH4 1134, modH5 2A, modH6 3A, modH7 CHP7, modH8 CHP2, modH9 CHP4, modH10 219, modH11 GN760, modH12 L252, modH13 L264, modH14 SouthAfrica7, modH15 Gambia 94/24, modH16 Cuz20 and modH17 908. To generate the amino acid sequences of the DRD region for this comparison the modH genes were translated, starting and ending with the residues corresponding to amino acid residues 214 and 449, respectively, with reference to the sequence of the H. pylori P12 type III methyltransferase (gb ACJ08645.1). (C) The 17 modH alleles are shown as coloured lines. BLASTn matches longer than 20 nucleotides and >90% identity between the 17 modH alleles were mapped as a box onto the corresponding allele in the appropriate colour. Detailed information on each individual coloured box is provided in Figure S1 and Table S1. (D) Diagrammatic representation of the tBLASTn match between modH3 and modH10. The nucleotides are represented as vertical bars (dark blue >90% identity; light blue >50% identity; white <50% identity or gap). The numbers below the figure indicate the percent identity as defined by BLASTn for the area between the double-headed arrows.
To investigate whether additional alleles of modH are present in H. pylori, and to examine the distribution of modH alleles and their repeat sequence type and number, sequence analysis of a genetically diverse set of H. pylori clinical isolates was performed. This analysis revealed that all strains examined contained the modH gene, with thirteen additional modH alleles observed, bringing to seventeen the total number of modH alleles observed (Table 1, Figure 1B). Here we define modH alleles of the same group as sharing more than 90% amino acid identity with other group members in a global pairwise alignment. In previous studies of mod genes inter-allelic diversity in the DNA recognition domain is very high with less than 30% amino acid identity shared by DNA recognition domain regions of different groups , . In contrast in comparison of the modH alleles, there are two groups of alleles (modH5/modH11/modH12 and modH3/modH10) that share large regions of high identity, separated by regions with little or no identity, a pattern suggestive of recombination. The most frequently occurring modH alleles observed in the strain survey are modH3 (16% of isolates tested) and modH5 (16% of isolates tested). Sequencing of the repeat region of the modH alleles revealed that the repeat numbers vary in length between 9 and 15 bp in different strains, resulting in the mod genes being in-frame (ON) or out-of-frame (OFF) for expression; consistent with phase-variation of the modH gene in this collection of strains (Table 1). Sequence analysis of the corresponding res genes in the strain collection revealed that strains F32 (modH2), and 52 (modH11) have nonsense mutations resulting in truncation of the res gene, while strain 51 (modH3) has a base pair missing resulting in a frame-shift mutation (Figure 1A, Table 1). Furthermore, for strains 2047 (modH2), L101 (modH3) and GN760 (modH11) a full-length res gene could not be amplified (Table 1).
Representatives of all 17 modH alleles were compared by multiple sequence alignment. Figure 1B illustrates the diversity seen throughout the DNA recognition domain of the modH alleles at the nucleotide level. There are several short regions of high similarity within the DNA recognition domain. The mosaic pattern observed in the alignment schematic (Figure 1B) suggests that large segments have been deleted or replaced via genetic recombination. To examine recombination within the DNA recognition domains in more detail and to determine its contribution to modH allele diversity, we undertook all versus all BLASTn searches using the 13 representative modH sequences (Figure 1C). The number of reciprocal exchanges identified gave a clear indication that the modH alleles have recombined in the past. By using this approach we identified new relationships between the modH alleles. Some alleles were found to have undergone recombination more readily than others to generate new alleles. For example, modH5, modH11 and modH12 share near identical 5′ and 3′ regions, but each has a different central fragment suggesting recent origin from an ancestral allele (Figure 1C). Closer examination of these regions reveals that the 5′ end of each allele (modH5, modH11 and modH12) matches the first 200 nucleotides of the other two alleles. For example, modH5 has matches to nucleotides 1–177 of modH11 and nucleotides 1–186 of modH12, modH11 has matches to modH5 (1–186) and modH12 (1–172) and modH12 has matches to modH5 (1–177) and modH11 (1–172) (Figure S1, Table S1). Similarly the 3′ end of modH5 has matches to regions related to modH11 (nucleotides 517–711) and modH12 (nucleotides 517–711) as well as modH4 (nucleotides 641–711), modH6 (nucleotides 647–711), modH8 (nucleotides 688–711) and modH16 (nucleotides 641–711) (Figure S1, Table S1). These regions of similarity are also observed in the 3′ ends of modH11 and modH12 (Figure S1, Table S1). Likewise, modH3 and modH10 also appear to have originated from a single allele that has undergone at least two recombination events to generate the diversity that now distinguishes them from one another (Figure 1D).
Analysis of differentially expressed genes in the H. pylori modH5 phasevarion
To determine whether phase-variation of the modH allele in H. pylori resulted in changes in global gene expression, we conducted a study using H. pylori strain P12, which expresses the most common modH5 allele. The modH5 gene was inactivated by insertion of a cat cassette to make the mutant strain P12ΔmodH5. Wild-type P12modH5 ON and P12ΔmodH5 were compared by microarray analysis using H. pylori P12 genome arrays (Methods). Six genes were found to be differentially expressed by a ratio of 1.6-fold or more, with 2 genes up-regulated in P12ΔmodH5 relative to wild-type and 4 genes down-regulated. These data confirmed that modH5 phase-variation has an influence on gene expression (Table 2). One gene with an increased expression of 2.4 fold in the modH mutant encodes the surface exposed protein, HopG (also known as HopY), a potential vaccine candidate . HopG is required for colonization  and may be associated with gastric cancer . Two genes associated with flagella showed increased expression in the modH ON strain. FlaA is the major component of the flagellar filament ,  and is required for normal motility, which is essential for colonization  and the establishment of persistent infection . HPP12_904 is homologous to the flagellar hook-length control protein FliK that is also essential for motility .
Quantitative real time PCR (QRT-PCR) confirmed that flaA and HPP12_904 were expressed at a higher level in the wild-type P12modH5 ON parent strain compared to P12ΔmodH5, while hopG and HPP12_0255 were expressed at a higher level in the P12ΔmodH5 mutant compared to P12modH5 ON (Table 2). QRT-PCR that compared the wild-type P12modH5 ON (G10) strain to a P12modH5 OFF strain (G6TG4), also confirmed the microarray results (Table 2).
We recently confirmed gene regulation as a function of phase-variable type III R-M systems in the human pathogens H. influenzae  and pathogenic Neisseria , thus defining a new paradigm in bacterial gene regulation “the phase-variable regulon; “phasevarion” . In this study we investigated whether the phase-variable type III R-M systems described in H. pylori serve a similar regulatory function.
H. pylori contain a number of phase-variable type II and type III R-M systems , , , as well as several active orphan type methyltransferases , , , suggesting that these methyltransferases may have functions other than restriction, such as gene regulation . Additionally, H. pylori strains have been found to have inactive type III and II res genes, indicating that DNA restriction may not be the function of phase-variable R-M systems , . Recently, methylation by a putative phase-variable mod gene associated with a type II R-M system in H. pylori (M.HpyAIV) was shown to influence gene expression of katA . The M.HpyAIV gene has also been associated with the induction of a more robust host response in mice, suggesting an involvement in gene regulation .
In type III R-M systems DNA sequence specificity is conferred by the Mod subunit . Differences in the modA DNA recognition domain have previously been observed in H. influenzae with 17 distinct modA alleles defined in this organism , . In pathogenic Neisseria, we identified three distinct modA alleles and two distinct modB alleles . Our phylogenetic studies on the modH gene of a collection of H. pylori clinical isolates revealed that there are 17 distinct modH alleles based on differences in their DNA recognition domain. In pathogenic Neisseria, strains with the same DNA recognition domain regulated the same set of genes, while those with different mod alleles regulate the expression of different sets of genes . Seventeen distinct modH alleles in H. pylori suggest that 17 distinct phasevarions exist. ModH3 and modH5 were the most frequent alleles observed in clinical isolates.
Further studies on the modH5 phasevarion were conducted using microarray to compare H. pylori strain P12, which expresses the modH5 allele, to a mutant strain. Of the genes regulated by the modH5 phasevarion, two encode proteins that have important roles in motility, FlaA and FliK. Motility is an essential factor for the colonization and persistence of H. pylori in the human stomach  and therefore flagella have an important role in virulence. In addition, H. pylori FlaA has low intrinsic capacity to activate innate immunity via the Toll-like receptor 5 , , . Therefore, altered expression of flagella may be advantageous for the adaptation of H. pylori to alternate host environments and in evading the host immune response. The gene encoding the essential outer membrane protein for colonization, HopG  was also found to be regulated by the modH5 phasevarion. Bacterial adherence mediated by HopG and outer membrane proteins is thought to play an important role in the colonization of the gastric epithelium by H. pylori , making HopG an attractive vaccine target . Hence phasevarion mediated phase-variation of hopG has the potential to mediate escape from the host immune response.
Only a relatively small number of genes were found to be under the control of the modH5 phasevarion. This may be the full extent of the regulon, or only be a sub-set of the regulon due to the analysis being done under standard in vitro culture conditions. Differences in gene expression can only be detected if the genes in question are being expressed. Using different physiologically relevant conditions, such as specific pH conditions that reflect the gastric environment, may result in more genes being found to be under the influence of the modH5 phasevarion.
Here we provide evidence for a role for phase-variable mod genes associated with type III R-M systems in gene regulation in H. pylori. Although we cannot exclude another as yet undescribed role for these modH phase variation in H. pylori biology, we have confirmed phasevarion mediated epigenetic mechanism of gene expression does operate in H. pylori. Further characterisation of this phasevarion will contribute to an improved understanding of H. pylori pathogenesis and may guide vaccine development for this important human pathogen by defining stably expressed immunological targets in modH5 strains. Based on our previous studies  it is likely that other H. pylori modH alleles also function as phasevarions and regulate gene expression. Future studies in H. pylori involving gene regulation, host/pathogen interactions or vaccine development need to control for the potential for modH phase variation to alter global gene expression.
Materials and Methods
Bacterial strains and growth 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 mg/ml; trimethoprim, 2.5 mg/ml; vancomycin, 10 mg/ml) in a microaerobic atmosphere as described previously . Plates for cultivation of mutant strains were further supplemented with chloramphenicol (4 mg/ml for routine culture, 10 mg/ml for selection of transformants).
DNA manipulation and analysis
All enzymes were sourced from New England Biolabs. Sequencing was performed on PCR products using QiaQuick PCR purification kit (Qiagen) and Big-Dye (Perkin Elmer) sequencing kits. Data were analysed using MacVector v11.0 (Accelrys).
ModH alleles (formerly called ModC ) were classified as ModH1-13 according to all-versus-all global pairwise amino acid alignments of the ModH DRD region and a within-group minimum identity cut-off of 90%. Global pairwise alignments were calculated with a dynamic programming technique as implemented in Jalview (http://www.jalview.org/) (alignment parameters: BLOSUM62 substitution matrix, gap-open penalty of 12, gap-extend penalty of 2). Inter-allele comparisons were carried out using all versus all BLASTn and BLASTp comparisons of representative ModH DRD alleles using stand-alone NCBI BLAST without filters (version 2.2.18). Amino acid and nucleotide sequences were aligned using ClustalX (version 2.0.11). Multiple alignments were viewed and edited in Jalview (42). The GenBank accession numbers are HQ734231–HQ734257, HQ830157–HQ830158 and JN974761–JN974763.
mod and res specific PCR
The modH gene and resH gene were amplified and sequenced using the primers listed in Table 3. H. pylori clinical isolates were used as templates (Table 1). The reaction was performed in 50 µl using KOD (Novagen) reagents, and 1 unit of KOD DNA polymerase with the following cycling conditions for the modH gene: 30 cycles of 94°C for 30 sec, 50°C for 30 sec, 70°C for 1 min and 1 cycle of 72°C for 5 min with 5 µM of the primer pair HP_MODHF1 and HP_MODHR5. A 693 bp region containing the DNA recognition domain (603 bp downstream of HP_MODHF1 and 640 bp upstream from HP_MODHR5) was compared to the H. pylori genome strains to determine the modH allele (Table 1). The primers HP_MODHREPEATF and HP_MODHR4 were used to sequence the repeat region. The resH gene was amplified using the primer pair HP_RESHF1 and HP_RESHR1 with the following cycling conditions: 30 cycles of 94°C for 30 sec, 50°C for 30 sec, 72°C for 2 min and 1 cycle of 72°C for 5 min. Only the regions containing the conserved motifs and nonsense mutations were sequenced using the primers HP_RESHF1, HP_RESHR1 and HP_RESHR7. PCR products were cleaned using the QIAquick PCR Purification Kit (Qiagen).
Construction of knockout mutant and OFF mutant of the modH5 gene of H. pylori strain P12
Two mutants of modH were made using strain H. pylori P12. In strain P12 the modH5 gene contains a G10 tract in the coding sequence of the gene and is in-frame for expression of a full-length modH gene; hence it is defined as “ON”. The complete ORF of P12modH5 was amplified using Vent DNA polymerase and primer pair RGRM4F/RGRMR4 and A-tailed before cloning into pGEM-T easy (Promega). The first mutant, P12ΔmodH5, was produced by allelic exchange of a 1480 bp region of modH containing the DNA binding region and poly-G tract, with a choloramphenicol resistance cassette (cat) lacking a transcriptional terminator . The cloned ORF was inversely amplified using primer pair RGRM4Fmut/RGRM4Rmut1 to excise the 1480 bp region and introduce BamHI sites, which were used to ligate BamHI-cut cat. The second mutant, P12modH5 OFF, carried an insertion in the polyG tract to alter it to N11, resulting in a frame-shift mutation to an “OFF” phase. The cloned ORF was inversely amplified using primer pair RGRMFmut2/RGRM4Rmut3 to insert a silent thymidine residue into the poly-G tract, changing G10, to 5′-GGGGGGTGGGG-3′, excising a 270 bp region, and introducing BamHI sites for ligation with BamHI-cut cat. Both mutagenesis constructs carried the cat cassette in the same orientation as modH. For transformation of H. pylori P12, the linear mutagenesis cassettes were amplified using primer pair RGRM4F/RGRM4R. Naturally competent P12 was transformed using the purified PCR product as described previously  and transformants were screened by sequence analysis.
Triplicate cultures of H. pylori strain wild-type P12modH5 ON, P12modH5 OFF and the P12ΔmodH5 mutant, were grown to exponential phase (optical density at 550 nm = 0.9) in BHI broth (Oxoid) supplemented with 10% (v/v) fetal bovine serum (Invitrogen), vitamin mix and vancomycin. Bacterial cells were stabilized using RNAprotect Bacteria Reagent (Qiagen) prior to RNA extraction and approximately 50 µg of total RNA was prepared from each sample using the RNeasy Maxi Kit according to the manufacturer's instructions (Qiagen). The integrity and concentration of RNA were determined via micro-fluidic analysis on a bio-analyser (Agilent Technologies).
Custom Agilent 8×15 k oligonucleotide microarrays (Agilent, CA, USA) were designed based on the publically available sequence of H. pylori P12 (NC_011498) using E-array (Agilent, CA, USA). Reverse transcription reactions were performed in 40 µl volumes, containing 10 µg total RNA, 300 ng random hexamers, 0.5 mM dNTPs and 300 U SuperScript III Reverse Transcriptase (Invitrogen) at 42°C for 2.5 h. RNA contamination was removed from the cDNA by the addition of NaOH followed by column purification (Qiagen minElute, Qiagen). A total of 1 µg of purified cDNA was labeled using KREAtech Cy3-ULS (KREAtech, The Netherlands), and 625 ng was used to hybridize Agilent 8×15 k microarrays as per the manufacturer's instructions.
Hybridized arrays were scanned on an Agilent Genepix G2565BA scanner, and features were extracted using Feature Extraction V9.5 (Agilent, CA, USA). Analysis was performed using LIMMA  as follows. Background correction was applied, spots from duplicate probes were averaged and log transformed. Between-array quantile normalization was then applied to the log transformed spot intensities. A moderated t-test on the normalized log intensities was performed to identify differentially expressed genes and the False Discovery Rate (FDR) used to control for multiple testing. Genes were ranked using the B-statistic (B-stat) method where both fold change and variance of signals in replicates are used to determine the likelihood that genes are truly differentially expressed. A threshold in the B- stat of 0.0 was adopted as genes with a B score >0 have a >50% probability of being truly differentially expressed . All experimental data are available online at the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) submission number GSE26759. All data is MIAME compliant.
Quantitative Real-Time PCR
Oligonucleotides (Table 3) were designed using Primer Express 1.0 software (ABI Prism; PE Biosystems) and are named according to the open reading frame (ORF) being amplified. All real-time PCR reactions were performed in a 25 µl mixture containing 1 in 5 dilution of cDNA preparation (5 µl), 10× SYBR Green buffer (PE Applied Biosystems) and 5 µM of each primer. We used 16S RNA as the control in each quantitative PCR. Amplification and detection of specific products were performed with the ABI Prism 7700 sequence-detection system (PE Applied Biosystems) with the following cycle profile: 95°C for 10 min, followed by 45 cycles of 95°C for 15 sec and 60°C for 1 min. Data were analyzed with ABI prism 7700 (version 1.7) analysis software. Relative gene expression between the P12ΔmodH5 mutant and wild-type P12modH5 ON and P12modH5 OFF and wild-type P12modH5 ON was determined using the 2ΔΔCT relative quantification method.
Diagrammatical representation of the 17 modH alleles of H. pylori. BLASTn was used to identify reciprocal exchanges between the modH DNA recognition domains of the following H. pylori strains (listed in Table 1); modH1 BH13, modH2 1061, modH3 11637, modH4 1134, modH5 2A, modH6 3A, modH7 CHP7, modH8 CHP2, modH9 CHP4, modH10 219, modH11 GN760, modH12 L252, modH13 L264, modH14 SouthAfrica7, modH15 Gambia 94/24, modH16 Cuz20 and modH17 908. Each unique modH DNA recognition domain is represented as a coloured box. BLASTn matches longer than 20 nt and >90% identity were mapped on to the corresponding allele in the appropriate colour. The number above the coloured boxes corresponds to Table S1 that contains details of the start and stop positions of each exchange. The nucleotide positions correspond to the DNA recognition domain only.
We are indebted to Drs J. Kusters and A van Vliet (Erasmus Medical Center, Rotterdam, The Netherlands) for providing us with clinical isolates of H. pylori clinical isolates from the Netherlands, Canada and Brazil.
Conceived and designed the experiments: MPJ. Performed the experiments: YNS RJG JAS JAG. Analyzed the data: YNS RJG JAS JAG. Contributed reagents/materials/analysis tools: MPJ RRB SMG TK. Wrote the paper: YNS MPJ. Obtained funding: MPJ RRB SMG. Revised the paper: YNS MPJ RRB RJG.
- 1. Moss SF, Sood S (2003) Helicobacter pylori. Curr Opin Infect Dis 16: 445–451.SF MossS. Sood2003Helicobacter pylori.Curr Opin Infect Dis16445451
- 2. Peek RM Jr, Crabtree JE (2006) Helicobacter infection and gastric neoplasia. J Pathol 208: 233–248.RM Peek JrJE Crabtree2006Helicobacter infection and gastric neoplasia.J Pathol208233248
- 3. Blaser MJ (1997) Ecology of Helicobacter pylori in the human stomach. J Clin Invest 100: 759–762.MJ Blaser1997Ecology of Helicobacter pylori in the human stomach.J Clin Invest100759762
- 4. Ernst PB, Gold BD (2000) The disease spectrum of Helicobacter pylori: the immunopathogenesis of gastroduodenal ulcer and gastric cancer. Annu Rev Microbiol 54: 615–640.PB ErnstBD Gold2000The disease spectrum of Helicobacter pylori: the immunopathogenesis of gastroduodenal ulcer and gastric cancer.Annu Rev Microbiol54615640
- 5. de Vries N, Duinsbergen D, Kuipers EJ, Pot RG, Wiesenekker P, et al. (2002) Transcriptional phase variation of a type III restriction-modification system in Helicobacter pylori. J Bacteriol 184: 6615–6623.N. de VriesD. DuinsbergenEJ KuipersRG PotP. Wiesenekker2002Transcriptional phase variation of a type III restriction-modification system in Helicobacter pylori.J Bacteriol18466156623
- 6. van Belkum A, Scherer S, van Alphen L, Verbrugh H (1998) Short-sequence DNA repeats in prokaryotic genomes. Microbiol Mol Biol Rev 62: 275–293.A. van BelkumS. SchererL. van AlphenH. Verbrugh1998Short-sequence DNA repeats in prokaryotic genomes.Microbiol Mol Biol Rev62275293
- 7. Moxon ER, Thaler DS (1997) Microbial genetics. The tinkerer's evolving tool-box. Nature 387: 659, 661–652.ER MoxonDS Thaler1997Microbial genetics. The tinkerer's evolving tool-box.Nature387659, 661652
- 8. Fox KL, Srikhanta YN, Jennings MP (2007) Phase variable type III restriction-modification systems of host-adapted bacterial pathogens. Mol Microbiol 65: 1375–1379.KL FoxYN SrikhantaMP Jennings2007Phase variable type III restriction-modification systems of host-adapted bacterial pathogens.Mol Microbiol6513751379
- 9. Srikhanta YN, Fox KL, Jennings MP (2010) The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes. Nat Rev Microbiol 8: 196–206.YN SrikhantaKL FoxMP Jennings2010The phasevarion: phase variation of type III DNA methyltransferases controls coordinated switching in multiple genes.Nat Rev Microbiol8196206
- 10. Bickle TA, Kruger DH (1993) Biology of DNA restriction. Microbiol Rev 57: 434–450.TA BickleDH Kruger1993Biology of DNA restriction.Microbiol Rev57434450
- 11. Boyer HW (1971) DNA restrictions and modification mechanisms in bacteria. Annu Rev Microbial 25 153–176: 153–176.HW Boyer1971DNA restrictions and modification mechanisms in bacteria.Annu Rev Microbial25 153–176153176
- 12. Bourniquel AA, Bickle TA (2002) Complex restriction enzymes: NTP-driven molecular motors. Biochimie 84: 1047–1059.AA BourniquelTA Bickle2002Complex restriction enzymes: NTP-driven molecular motors.Biochimie8410471059
- 13. Meisel A, Mackeldanz P, Bickle TA, Kruger DH, Schroeder C (1995) Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. Embo J 14: 2958–2966.A. MeiselP. MackeldanzTA BickleDH KrugerC. Schroeder1995Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis.Embo J1429582966
- 14. Bachi B, Reiser J, Pirrotta V (1979) Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme. J Mol Biol 128: 143–163.B. BachiJ. ReiserV. Pirrotta1979Methylation and cleavage sequences of the EcoP1 restriction-modification enzyme.J Mol Biol128143163
- 15. Humbelin M, Suri B, Rao DN, Hornby DP, Eberle H, et al. (1988) Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutants. J Mol Biol 200: 23–29.M. HumbelinB. SuriDN RaoDP HornbyH. Eberle1988Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutants.J Mol Biol2002329
- 16. Srikhanta YN, Maguire TL, Stacey KJ, Grimmond SM, Jennings MP (2005) The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes. Proc Natl Acad Sci U S A 102: 5547–5551.YN SrikhantaTL MaguireKJ StaceySM GrimmondMP Jennings2005The phasevarion: a genetic system controlling coordinated, random switching of expression of multiple genes.Proc Natl Acad Sci U S A10255475551
- 17. Srikhanta YN, Dowideit SJ, Edwards JL, Falsetta ML, Wu HJ, et al. (2009) Phasevarions mediate random switching of gene expression in pathogenic Neisseria. PLoS Pathog 5: e1000400.YN SrikhantaSJ DowideitJL EdwardsML FalsettaHJ Wu2009Phasevarions mediate random switching of gene expression in pathogenic Neisseria.PLoS Pathog5e1000400
- 18. Peck B, Ortkamp M, Nau U, Niederweis M, Hundt E, et al. (2001) Characterization of four members of a multigene family encoding outer membrane proteins of Helicobacter pylori and their potential for vaccination. Microbes Infect 3: 171–179.B. PeckM. OrtkampU. NauM. NiederweisE. Hundt2001Characterization of four members of a multigene family encoding outer membrane proteins of Helicobacter pylori and their potential for vaccination.Microbes Infect3171179
- 19. Kavermann H, Burns BP, Angermuller K, Odenbreit S, Fischer W, et al. (2003) Identification and characterization of Helicobacter pylori genes essential for gastric colonization. J Exp Med 197: 813–822.H. KavermannBP BurnsK. AngermullerS. OdenbreitW. Fischer2003Identification and characterization of Helicobacter pylori genes essential for gastric colonization.J Exp Med197813822
- 20. Giannakis M, Chen SL, Karam SM, Engstrand L, Gordon JI (2008) Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells. Proc Natl Acad Sci U S A 105: 4358–4363.M. GiannakisSL ChenSM KaramL. EngstrandJI Gordon2008Helicobacter pylori evolution during progression from chronic atrophic gastritis to gastric cancer and its impact on gastric stem cells.Proc Natl Acad Sci U S A10543584363
- 21. Suerbaum S, Josenhans C, Labigne A (1993) Cloning and genetic characterization of the Helicobacter pylori and Helicobacter mustelae flaB flagellin genes and construction of H. pylori flaA- and flaB-negative mutants by electroporation-mediated allelic exchange. J Bacteriol 175: 3278–3288.S. SuerbaumC. JosenhansA. Labigne1993Cloning and genetic characterization of the Helicobacter pylori and Helicobacter mustelae flaB flagellin genes and construction of H. pylori flaA- and flaB-negative mutants by electroporation-mediated allelic exchange.J Bacteriol17532783288
- 22. Kostrzynska M, Betts JD, Austin JW, Trust TJ (1991) Identification, characterization, and spatial localization of two flagellin species in Helicobacter pylori flagella. J Bacteriol 173: 937–946.M. KostrzynskaJD BettsJW AustinTJ Trust1991Identification, characterization, and spatial localization of two flagellin species in Helicobacter pylori flagella.J Bacteriol173937946
- 23. Josenhans C, Labigne A, Suerbaum S (1995) Comparative ultrastructural and functional studies of Helicobacter pylori and Helicobacter mustelae flagellin mutants: both flagellin subunits, FlaA and FlaB, are necessary for full motility in Helicobacter species. J Bacteriol 177: 3010–3020.C. JosenhansA. LabigneS. Suerbaum1995Comparative ultrastructural and functional studies of Helicobacter pylori and Helicobacter mustelae flagellin mutants: both flagellin subunits, FlaA and FlaB, are necessary for full motility in Helicobacter species.J Bacteriol17730103020
- 24. Eaton KA, Suerbaum S, Josenhans C, Krakowka S (1996) Colonization of gnotobiotic piglets by Helicobacter pylori deficient in two flagellin genes. Infect Immun 64: 2445–2448.KA EatonS. SuerbaumC. JosenhansS. Krakowka1996Colonization of gnotobiotic piglets by Helicobacter pylori deficient in two flagellin genes.Infect Immun6424452448
- 25. Ryan KA, Karim N, Worku M, Penn CW, O'Toole PW (2005) Helicobacter pylori flagellar hook-filament transition is controlled by a FliK functional homolog encoded by the gene HP0906. J Bacteriol 187: 5742–5750.KA RyanN. KarimM. WorkuCW PennPW O'Toole2005Helicobacter pylori flagellar hook-filament transition is controlled by a FliK functional homolog encoded by the gene HP0906.J Bacteriol18757425750
- 26. Alm RA, Ling LS, Moir DT, King BL, Brown ED, et al. (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397: 176–180.RA AlmLS LingDT MoirBL KingED Brown1999Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.Nature397176180
- 27. Doig P, de Jonge BL, Alm RA, Brown ED, Uria-Nickelsen M, et al. (1999) Helicobacter pylori physiology predicted from genomic comparison of two strains. Microbiol Mol Biol Rev 63: 675–707.P. DoigBL de JongeRA AlmED BrownM. Uria-Nickelsen1999Helicobacter pylori physiology predicted from genomic comparison of two strains.Microbiol Mol Biol Rev63675707
- 28. Lin LF, Posfai J, Roberts RJ, Kong H (2001) Comparative genomics of the restriction-modification systems in Helicobacter pylori. Proc Natl Acad Sci U S A 98: 2740–2745.LF LinJ. PosfaiRJ RobertsH. Kong2001Comparative genomics of the restriction-modification systems in Helicobacter pylori.Proc Natl Acad Sci U S A9827402745
- 29. Kong H, Lin LF, Porter N, Stickel S, Byrd D, et al. (2000) Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome. Nucleic Acids Res 28: 3216–3223.H. KongLF LinN. PorterS. StickelD. Byrd2000Functional analysis of putative restriction-modification system genes in the Helicobacter pylori J99 genome.Nucleic Acids Res2832163223
- 30. Vitkute J, Stankevicius K, Tamulaitiene G, Maneliene Z, Timinskas A, et al. (2001) Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695. J Bacteriol 183: 443–450.J. VitkuteK. StankeviciusG. TamulaitieneZ. ManelieneA. Timinskas2001Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695.J Bacteriol183443450
- 31. Skoglund A, Bjorkholm B, Nilsson C, Andersson A, Jernberg C, et al. (2007) Functional analysis of the M.HpyAIV DNA-methyltransferase of Helicobacter pylori. J Bacteriol 189: 8914–8921.A. SkoglundB. BjorkholmC. NilssonA. AnderssonC. Jernberg2007Functional analysis of the M.HpyAIV DNA-methyltransferase of Helicobacter pylori.J Bacteriol18989148921
- 32. Bjorkholm BM, Guruge JL, Oh JD, Syder AJ, Salama N, et al. (2002) Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a correlation between host responses and HsdS components of type I restriction-modification systems. J Biol Chem 277: 34191–34197.BM BjorkholmJL GurugeJD OhAJ SyderN. Salama2002Colonization of germ-free transgenic mice with genotyped Helicobacter pylori strains from a case-control study of gastric cancer reveals a correlation between host responses and HsdS components of type I restriction-modification systems.J Biol Chem2773419134197
- 33. Bayliss CD, Callaghan MJ, Moxon ER (2006) High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. Nucleic Acids Res 34: 4046–4059.CD BaylissMJ CallaghanER Moxon2006High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae.Nucleic Acids Res3440464059
- 34. Fox KL, Dowideit SJ, Erwin AL, Srikhanta YN, Smith AL, et al. (2007) Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression. Nucleic Acids Res 35: 5242–5252.KL FoxSJ DowideitAL ErwinYN SrikhantaAL Smith2007Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression.Nucleic Acids Res3552425252
- 35. Andersen-Nissen E, Smith KD, Strobe KL, Barrett SL, Cookson BT, et al. (2005) Evasion of Toll-like receptor 5 by flagellated bacteria. Proc Natl Acad Sci U S A 102: 9247–9252.E. Andersen-NissenKD SmithKL StrobeSL BarrettBT Cookson2005Evasion of Toll-like receptor 5 by flagellated bacteria.Proc Natl Acad Sci U S A10292479252
- 36. Gewirtz AT, Yu Y, Krishna US, Israel DA, Lyons SL, et al. (2004) Helicobacter pylori flagellin evades toll-like receptor 5-mediated innate immunity. J Infect Dis 189: 1914–1920.AT GewirtzY. YuUS KrishnaDA IsraelSL Lyons2004Helicobacter pylori flagellin evades toll-like receptor 5-mediated innate immunity.J Infect Dis18919141920
- 37. Lee SK, Stack A, Katzowitsch E, Aizawa SI, Suerbaum S, et al. (2003) Helicobacter pylori flagellins have very low intrinsic activity to stimulate human gastric epithelial cells via TLR5. Microbes Infect 5: 1345–1356.SK LeeA. StackE. KatzowitschSI AizawaS. Suerbaum2003Helicobacter pylori flagellins have very low intrinsic activity to stimulate human gastric epithelial cells via TLR5.Microbes Infect513451356
- 38. Bernarde C, Lehours P, Lasserre JP, Castroviejo M, Bonneu M, et al. (2010) Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism. Mol Cell Proteomics 9: 2796–2826.C. BernardeP. LehoursJP LasserreM. CastroviejoM. Bonneu2010Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism.Mol Cell Proteomics927962826
- 39. Gorrell RJ, Yang J, Kusters JG, van Vliet AH, Robins-Browne RM (2005) Restriction of DNA encoding selectable markers decreases the transformation efficiency of Helicobacter pylori. FEMS Immunol Med Microbiol 44: 213–219.RJ GorrellJ. YangJG KustersAH van VlietRM Robins-Browne2005Restriction of DNA encoding selectable markers decreases the transformation efficiency of Helicobacter pylori.FEMS Immunol Med Microbiol44213219
- 40. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.GK Smyth2004Linear models and empirical bayes methods for assessing differential expression in microarray experiments.Stat Appl Genet Mol Biol3Article3
- 41. Smyth GK, Yang YH, Speed T (2003) Statistical issues in cDNA microarray data analysis. Methods Mol Biol 224: 111–136.GK SmythYH YangT. Speed2003Statistical issues in cDNA microarray data analysis.Methods Mol Biol224111136
- 42. Fischer W, Windhager L, Rohrer S, Zeiller M, Karnholz A, et al. (2010) Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer. Nucleic Acids Res 38: 6089–6101.W. FischerL. WindhagerS. RohrerM. ZeillerA. Karnholz2010Strain-specific genes of Helicobacter pylori: genome evolution driven by a novel type IV secretion system and genomic island transfer.Nucleic Acids Res3860896101