- Research article
- Open Access
Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates
© Hovey et al; licensee BioMed Central Ltd. 2007
- Received: 22 November 2006
- Accepted: 04 April 2007
- Published: 04 April 2007
Clinical isolates of the gastric pathogen Helicobacter pylori display a high level of genetic macro- and microheterogeneity, featuring a panmictic, rather than clonal structure. The ability of H. pylori to survive the stomach acid is due, in part, to the arginase-urease enzyme system. Arginase (RocF) hydrolyzes L-arginine to L-ornithine and urea, and urease hydrolyzes urea to carbon dioxide and ammonium, which can neutralize acid.
The degree of variation in arginase was explored at the DNA sequence, enzyme activity and protein expression levels. To this end, arginase activity was measured from 73 minimally-passaged clinical isolates and six laboratory-adapted strains of H. pylori. The rocF gene from 21 of the strains was cloned into genetically stable E. coli and the enzyme activities measured. Arginase activity was found to substantially vary (>100-fold) in both different H. pylori strains and in the E. coli model. Western blot analysis revealed a positive correlation between activity and amount of protein expressed in most H. pylori strains. Several H. pylori strains featured altered arginase activity upon in vitro passage. Pairwise alignments of the 21 rocF genes plus strain J99 revealed extensive microheterogeneity in the promoter region and 3' end of the rocF coding region. Amino acid S232, which was I232 in the arginase-negative clinical strain A2, was critical for arginase activity.
These studies demonstrated that H. pylori arginase exhibits extensive genotypic and phenotypic variation which may be used to understand mechanisms of microheterogeneity in H. pylori.
- Clinical Isolate
- Urease Activity
- Pylorus Strain
Helicobacter pylori, a Gram negative bacterium, is a highly host-adapted gastric pathogen that has been implicated in a wide spectrum of diseases ranging from gastritis to adenocarcinoma [1–5]. Although this bacterium colonizes the gastric mucosa of billions of people, only 20% of the infected people become symptomatic. The disparities of symptoms from one person to another are indicative of a pathogen with significant genetic diversity. Two major types of diversity have been described in H. pylori clinical isolates: i) macrohetereogeneity, in which large chromosomal regions vary from strain to strain, and ii) microheterogeneity, in which individual genes feature sequence diversity. Examples of macroheterogeneity include the presence or absence of the cag pathogenicity island, insertion sequences, and a hypervariable region containing about half of the strain-specific genes, called the plasticity zone [6–14]. Furthermore, 22% of the organism's genes are dispensable in one or more strains, leading to a core of only about 1280 genes . Macroheterogeneity can be assessed by restriction fragment length polymorphisms, multilocus enzyme electrophoresis, and microarrays.
Examples of microheterogeneity include extensive sequence variation of the vacA, cagA, babA, hopQ, iceA genes and other genes [9, 15–20]. For example, the vacA gene encoding the vacuolating cytotoxin (VacA) exhibits a remarkable degree of genotypic and phenotypic variation [9, 21–23]. The vacuolating activity of VacA varies approximately 30-fold across different isolates due to the presence of at least five different vacA alleles . Two families of the vacA alleles, type m1 and type m2, are only about 70% identical . In addition, there is also evidence that mixed strain infections can occur in a single patient , and that a single strain can change in vivo over time [16, 27, 28]. The extraordinary diversity of this pathogen may explain why the acquired immune response cannot clear the infection or prevent reinfection by a heterologous strain. The genetic variation among the bacterium's virulence factors may relate to the diverse disease manifestations in patients, although this is not well understood.
On the other hand, the urease structural proteins, UreA and UreB, are very well conserved across heterologous strains of H. pylori (97–100% amino acid identity, based on BlastP analysis of GenBank sequences). These proteins constitute a nickel-requiring, highly abundant metalloenzyme that is central to the pathogenesis of the bacterium . Urease hydrolyzes urea to carbon dioxide and ammonia, the latter of which neutralizes gastric acid . Local neutralization of gastric acid helps H. pylori to safely traverse the gastric mucosal layer and colonize the gastric epithelium . Indeed, urease mutants are unable to colonize and establish a lasting infection in nude mice and gnotobiotic piglets [32–34]. Considering that functional urease is absolutely essential for virulence, numerous random mutations in the functional core of the urease gene could be detrimental, thus explaining why ureA and ureB are highly conserved in heterologous strains. Without stability in these two structural genes, this species would be ineffective as a pathogen.
The source of urea for H. pylori urease can either be through host- or bacterial-derived arginase. H. pylori contains the rocF gene encoding arginase, which catalyzes the hydrolysis of L-arginine to L-ornithine and urea [35–37]. H. pylori is deficient in the enzymes for synthesizing arginine de novo and is therefore dependent on host arginine to help it maintain nitrogen balance [36–38]. Arginase consumes arginine, thereby removing this essential amino acid away from other cellular processes if the enzyme activity is too high. The role of arginase in H. pylori pathogenesis is beginning to be unraveled. Arginase allows the bacterium to evade host immune response by competing with macrophage inducible nitric oxide synthase (iNOS) for L-arginine . H. pylori arginase also down-regulates expression of CD3ς on T-cells, preventing their proliferation via consumption of arginine from the extracellular milieu . Moreover, arginase produces endogenous urea that can be hydrolyzed by urease to produce ammonium that contributes to acid resistance . Thus, arginase is involved in helping H. pylori evade both the innate (acid, NO) and adaptive (T cells) immune systems. Arginase clearly plays a role in these pathogenic processes, but surprisingly the rocF gene encoding arginase is not essential for the establishment of infection , suggesting that in vivo the enzyme plays a role downstream of the initial colonization step, perhaps modulating disease severity.
The importance of specific mutations in the phenotypic variation of this species are largely unknown. The evolution of specific genes and proteins in this pathogen are of paramount importance as the field strives to understand the role of specific genes in virulence. In a previous study involving laboratory-adapted strains, some variation in arginase activity was found among three strains . However, it was not determined whether this variation occurred from spontaneous mutation from passaging the strains repeatedly in the laboratory or from natural diversity existing among H. pylori strains. To determine arginase variability, phenotypic and genotypic analyses of rocF in 73 minimally-passaged clinical isolates and six laboratory-adapted strains was investigated. While most previous studies on microheterogeneity focused on only a small portion of a gene, we studied the entire arginase coding region plus upstream region. This study demonstrates that extensive microheterogeneity exists in the rocF gene, with phenotypic manifestations, and provides evidence that this gene may serve as a model to study microheterogeneity in H. pylori.
Variation of arginase activity in clinical isolates of H. pylori
To determine whether an alternative growth medium also resulted in variable arginase activity, H. pylori strains were grown in Ham's F-12 broth and corresponding extracts assayed for arginase activity. Arginase activity also varies in broth, depending on the strain, but there was a strong correlation (correlation coefficient= 0.9) between arginase activity of a particular strain in broth versus agar (Fig. 1B). In other words, strains with low arginase activity on agar also had low arginase activity in broth.
Although we previously determined that rocF mutants of H. pylori have wild type levels of urease activity , we sought to determine whether arginase and urease activities correlated, using a larger number of strains. Twelve clinical isolates of H. pylori were measured for urease activity and compared with arginase activity. Notably, there was more than 25-fold variation in urease activity among clinical isolates examined (Fig. S1A, see additional file 2). Variation in urease activity in fresh clinical isolates was 3–10-fold in previous studies using less sensitive urease activity methods [41, 42]. There was no correlation whatsoever between urease and arginase activities (correlation coefficient = 0.04) (Fig. S1B, see additional file 2). For example, some strains had low arginase but high urease activties while other strains had low activities of both enzymes.
E. coli expressing the arginase gene from different H. pylori clinical isolates displays variable activity
The variation in arginase enzyme activity observed in H. pylori could be due to sequence differences in the arginase protein itself or in other loci which may affect the enzyme. To eliminate the genetic variability of other H. pylori loci as a compounding factor, arginase activity was assessed in the genetically stable E. coli model developed previously . The arginase gene with its native promoter from 20 of the strains used in this study, representing low, intermediate and high arginase activities, was cloned into pBluescript and arginase activity measured in transformed E. coli. (Although the rocF gene from strain G27 was cloned and sequenced, arginase activity from E. coli carrying this clone was not directly compared to the others, because the rocF gene was in a different plasmid and strain of E. coli from the rest of the clones. However, the G27 rocF did confer arginase activity to E. coli Top10 [14,200 U versus 700 U in insert-free vector control strain pCR2.1). Remarkably, arginase activity depended on the particular arginase gene cloned into E. coli, with a greater than 100-fold magnitude of variation (Fig. S2, see additional file 3). Surprisingly, there was absolutely no correlation (r2 = 0.0749) between the arginase activity from E. coli containing a particular rocF gene and the arginase activity of the H. pylori strain from which the rocF gene was cloned (data not shown). For example, H. pylori strain A5 has almost no detectable arginase activity, yet the rocF gene from this strain conferred arginase activity to E. coli. H. pylori strain A4 has one of the highest arginase activities among all the clinical isolates (4431 U), yet its arginase gene conferred among the lowest arginase activities to E. coli. Thus, the data also raise the possibility that there are strain-specific H. pylori loci that modulate arginase activity. We hesitate to make other firm conclusions due to plasmid copy number effects potentially having an influence on the arginase activity levels observed.
Evidence for strain-specific regulation of H. pylori arginase activity
Disruption of the rocF gene results in abolishment of arginase activity [35, 44]. A new chromosomal complementation system for H. pylori that targets the hp0203-204 intergenic region demonstrated that the arginase mutant of strain 26695 could be complemented for arginase activity .
Additional evidence for strain-dependent arginase activity was revealed from strains SS1, B5 and B1, which all have identical rocF coding regions and upstream regions, yet have different arginase activities (8100, 1900, 1400 U, respectively) (Table S1 in additional file 1).
Evidence that H. pylori prefers low to moderate arginase activity
Western Blot analysis of arginase in clinical isolates of H. pylori
Nucleotide, amino acid and phylogenetic analyses of rocF/RocF
Pairwise alignments of the translated RocF coding regions showed that they were 92% to 100% identical, with most variability located near the carboxy terminus (Fig. 5A). There were 42 amino acid residues out of 322 (13%) that were not 100% conserved across all the isolates. Of these 42, 28 of the variable residues are found in the last 100 amino acids, with nine of these variable sites being in the final 16 amino acids at the C-terminal end. Three strains, SS1, B5, and B1, were 100% identical at the nucleotide and amino acid levels. Strains HPDJM17 and J188 had five amino acid differences. All H. pylori RocF proteins were predicted to have 322 amino acids.
A phylogenetic tree of the arginase proteins from 23 H. pylori strains revealed four clades, with 16, 4, 2, or 1 strain(s) in the clades (Fig. 5D). A phylogenetic tree of the nucleotide sequences of the arginase upstream region from 22 H. pylori strains (strain AG1 excluded) showed three major clades containing one, fifteen and six strains, respectively (Fig. 5E). The two phylogenetic trees (Fig. 5D, 5E) showed little congruence with each other. For example, the RocF protein from strains 43504 and A4 were within the same clade, but the corresponding rocF upstream regions were in different clades. Two strains showing 100% identity in the arginase upstream region were strains G27 and B7, two of the highest arginase activity strains (3900 U and 4800 U, respectively) (Fig. 5C, 5E). These two strains did not have identical coding regions, showing 96% identity at the amino acid level. Three other strains were 100% identical in the upstream region: B5, SS1, and B1 (Fig. 5C, D). These three strains were also 100% identical at the amino acid level (Fig. 5D), yet had different levels of arginase activity (Fig. 5C). This provided additional evidence that a strain-specific locus other than rocF plays a role in some of the variability observed. No clear correlation could be made between phylogenetic placement on either of the trees (Fig. 5D, E) and the level of arginase activity (Table S1 in additional file 1).
Serine 232 in RocF is required for arginase activity
In this study the phenotypic and genotypic heterogeneity of arginase in 73 clinical isolates and six laboratory-adapted strains of H. pylori was investigated. Phenotypically, arginase activity varied more than 100-fold in both H. pylori (Fig. 1) and the E. coli model (Fig. S2 in additional file 3). Nearly all of the H. pylori strains featured intermediate or low arginase activities (77 of 79 strains). Of the five strains with the highest arginase activity, four were laboratory strains that have been passaged heavily. Notably, even the highest arginase activity strains (3401 and SS1 laboratory strains) have specific activities more than 10-fold lower than those measured for other bacterial and eukaryotic arginases (McGee, unpublished data). Arginine is a critical amino acid for several cellular processes, such as protein synthesis, and H. pylori absolutely requires arginine for growth [47–49]. The bacterium would rapidly hydrolyze the arginine if it had a high specific activity arginase, potentially depleting intracellular pools and starving itself of this essential amino acid. The few high arginase activity H. pylori strains may have compensatory mechanisms to overcome potential arginine starvation from the higher level of arginine hydrolysis. Two possible mechanisms are that the high arginase activity strains might have a higher affinity arginine transporter that would allow higher intracellular accumulation of arginine. Alternatively, the high arginase activity strains could have decreased arginine decarboxylase activity, another arginine-consuming enzyme that could also cause arginine depletion in H. pylori.
H. pylori is a heterogeneous species [23, 50] that features diversity at many levels. For example, there are many contingency genes that undergo phase variation through DNA slipped-strand mispairing of repeats, such as LPS biosynthesis genes, and genes encoding outer-membrane proteins . As another example of diversity, adhesion of H. pylori to fucosylated Lewis B antigens on the surface of the gastric epithelium appears to be dependent on variability of the babA gene. This gene shows much conservation in the 5' and 3' regions but large variability in its midregions . The cagA gene, encoded by the cag pathogenicity island, exhibits nucleotide sequences that are 92.8% conserved, with much diversity at the 3' end where an EPIYA amino acid repeat element is encoded [53, 54]. RocF also features diversity in its C-terminal region, although there are no repeat elements. RocF appears to more divergent than urease subunits A and B, but less divergent than CagA or VacA. Since rocF participates in various aspects of H. pylori pathogenesis [39, 40] and the gene displays remarkable heterogeneity shown in this study, it is possible that rocF heterogeneity may correlate with specific aspects of the pathogenesis of the bacterium, such as inhibition of nitric oxide production and T-cell proliferation. The data obtained do not provide evidence for a correlation between arginase activity and urease activity or between arginase activity and the disease status of the patient, although more isolates would need to be studied since there were few isolates available for certain disease categories. Moreover, a greater geographic distribution of strains also would be necessary.
The data support the hypothesis that some H. pylori strains may have strain-specific arginase gene regulation. For example, strain A5 has minimal to no detectable arginase activity in the native H. pylori strain, but significant activity was detected in E. coli transformed with the A5 rocF gene, suggesting that H. pylori strain A5 has an arginase repressor. Such a repressor may be inoperative, inefficient, or absent in high arginase activity strains such as 3401. Additionally, evidence for potential strain-specific arginase regulation was observed in H. pylori directly. Specifically, arginase activity of H. pylori strain J63 is low, but when the rocF gene from this strain was used to complement a rocF mutant of strain 26695 in single copy on the chromosome, a surprisingly elevated arginase phenotype was observed, suggesting that strain 26695 has an activator protein absent in strain J63 or strain J63 has a repressor protein absent from strain 26695. A possible molecular basis for this potential variation may be due to the hypervariablity in the upstream region, which displays variation in the Shine-Dalgarno (SD) region, as well as variation in the region shown by DNAse footprinting experiments to be bound by the ArsR regulator . Mutations in the upstream region could either affect transcriptional expression, or translational control through changes in strength of the SD sequence. Evidence in the literature also supports the rocF gene being regulated at the transcriptional level by acid  and by the two-component system ArsS/R (Hp0165/0166) . Strain-specific transcriptional and translation regulation mechanisms are not mutually exclusive.
Besides the hypothesized strain-specific arginase transcriptional and translation regulation, evidence was obtained that variations in the rocF sequence themselves play a key role in arginase activity, using the genetically stable E. coli model. E. coli is arginase negative, but when the H. pylori arginase genes were cloned into E. coli, variable arginase activity occurs. Since enzyme activity varied dramatically with the particular arginase gene cloned into E. coli, variations in the rocF sequence would also be responsible for at least some of the arginase phenotypic variation. H. pylori strain-specific regulators that could affect arginase transcription in native H. pylori strains most likely would be absent in the E. coli model. Pairwise alignments of rocF nucleotide sequences revealed significant microheterogeneity in the 3' end of the coding regions, and translation of these regions showed that RocF varies in the carboxy terminus. Variations near the C-terminus could possibly affect the folding of the arginase active site, thereby accounting for some of the arginase activity variation.
Evidence for the direct involvement of the rocF coding region in arginase activity variation was obtained from site-directed mutagenesis results. Specifically, mutation of serine 232 to isoleucine in RocF from strain 26695 completely abolished arginase activity, helping to explain why H. pylori strain A2, which has isoleucine in position 232 in its native arginase, showed barely detectable arginase activity. Thus, amino acid 232 appears to play a crucial role in arginase activity. Notably, the rocF gene from strain A2 conferred the lowest arginase activity to E. coli among the 20 rocF genes examined (Fig. S2 in Additional file 3). The possibility that other amino acid residues, or nucleotides in the rocF upstream region also play a role in the arginase null phenotype of strain A2 cannot be ruled out. Future experiments will endeavor to elucidate the mechanism of why serine 232 is so critical for arginase activity, as there is no prior precedent for a serine being required for arginase activity.
Evidence was also obtained that arginase activity could vary upon in vitro passage of some strains; the mechanism of this variation remains undefined. That the phylogenetic trees of the arginase promoter and the arginase protein bore little resemblance to each other suggested that each region is evolving via independent selective pressures. The greater nucleotide variability among arginase upstream regions compared with the coding regions suggests that the former has a higher mutation rate and more tolerance to nucleotide changes during selection of those mutations.
It was established that arginase varies genotypically and phenotypically among minimally-passaged clinical H. pylori isolates. Future work could center on understanding in greater detail the molecular basis of arginase activity variation, and identifying strain-specific arginase regulators. This would lead to improved understanding of the mechanisms by which H. pylori genes undergo changes leading to microheterogeneity as the organism strives to survive in its seemingly inhospitable gastric niche.
Bacterial strains, growth conditions, and plasmids
All H. pylori strains were cultured on Campylobacter agar containing 10% defibrinated sheep blood (CBA) at 37°C for 48 h in a microaerobic environment (5% O2/10%CO2/85% N2) in humidified air. For broth conditions, H. pylori strains were inoculated at 4 × 106 CFU/ml as determined by ATP assay  into 25 ml Ham's F-12  with 2% fetal bovine serum and grown without aeration for 16–18 h in a microaerobic environment. The minimally-passaged clinical isolates were obtained from Richard Peek (Vanderbilt University, 15 isolates), George Mendz (University of Sydney, Australia, 40 isolates), Barbara Schneider (Louisiana State University, New Orleans, 17 Colombian isolates) and one previously described clinical isolate (HPDJM17)  (Table S1 in additional file 1). The laboratory-adapted strains were SS1, 43504, 26695, J99, G27 and 3401. All isolates were passaged fewer than five times from the frozen stock, except in cases in which the effects of in vitro passage on arginase activity were studied.
E. coli strain DH5α was used for cloning and transformation procedures and XL1-Blue MRF' was utilized for the pQE30-based plasmids used in this study. E. coli was grown on Luria (L) agar and L broth plus appropriate antibiotics (ampicillin, 100 μg/ml; tetracycline, 15 μg/ml) at 37°C. Plasmid pBS [pBluescript II SK (+); Stratagene] was used for cloning rocF genes.
Preparation of arginase or urease-containing cell extracts
H. pylori and E. coli were harvested in 0.9% NaCl and sonicated in an ice-bath (two pulses at 25% intensity, 30 sec each with 30 sec rest between pulses). Following centrifugation (12,000 × g, two min, 4°C), the supernatants were retained on ice until measurement of arginase activity. Protein concentrations were determined by the bicinchoninic acid method using bovine serum albumin as a standard (Pierce, Rockford, IL).
Arginase activity assay
Arginase activity was measured using a colorimetric arginase assay developed and validated previously . The extracts were heat-activated (50°C, 30 min) in the presence of 5 mM cobaltous chloride to provide the enzyme with its required metal cofactor, followed by incubation in the presence of 15 mM MES-10 mM arginine buffer (pH 6.0) for 1 h at 37°C. The ornithine produced was detected spectrophotometrically at 515 nm in the presence of acidified ninhydrin (4 mg/ml). Data are presented as mean arginase specific activity (1 Unit (U) = 1 pmol L-ornithine produced per minute per milligram protein).
Urease activity assay
Urease activities were measured using the phenol-hypochlorite method as described previously .
SDS-PAGE and Western blot analysis of arginase extracts
Bacterial proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) using a 12% resolving gel and 10 μg of protein loaded per lane. These electrophoresed proteins were then transferred to methanol-treated polyvinylidene difluoride membrane using the Trans-blot cell transfer system (Bio-Rad). The blots were subsequently blocked in 5% (w/v) nonfat dry milk in Tris-buffered saline containing 0.5% (v/v) Tween-20 (TBST-1), and incubated with the primary RocF antiserum (1:2,500) for 2 h . After three washes with TBS containing 0.05% (v/v) Tween-20 (TBST-2), goat anti-rabbit IgG-conjugated alkaline phosphatase (Sigma Immunochemical Co.; 1:5,000 to 1:7,500) was added and incubated for 90 min. Following a triple wash with TBST-2, the blot was equilibrated with glycine buffer (100 mM glycine, 1 mM ZnCl2, 0.05% (w/v) sodium azide, and 1 mM MgCl2, pH 10.4). To develop the blot, 3-indoxyl phosphate (10 μg/ml) and nitroblue tetrazolium (100 μg/ml) in glycine buffer were used.
Molecular biology techniques
Plasmid DNA was extracted by column chromatography (Qiagen) or by alkaline lysis . Restriction endonuclease and ligation reactions were conducted according to the manufacturer's guidelines (Promega). PCR reactions (50 μl) contained 50–250 ng of DNA, 1–2 mM MgSO4, 0.20–0.25 mM dNTPs, 200 pmol of each primer, 2.5 U of Pfx polymerase (Invitrogen) and 10× Pfx polymerase buffer (Invitrogen). E. coli was transformed by the heat shock CaCl2 method.
Cloning of rocF into pBS
The rocF gene from clinical isolates and laboratory-adapted strains was PCR-amplified using the primers RocF-F27 (gcctgcag TCAAAAACTTGAATGGTTTTACTCTTT; Pst I site underlined; non-rocF sequence in lower case) and RocF-R28 (ggatcgat GTTTGGTTTGAAAAGCGATCA; Cla I site underlined; non-rocF sequence in lower case). The conditions for PCR amplification were set at 94°C for 5 minutes; [94°C, 15 seconds; 52°C, 30 seconds; 68°C, 1 minute 30 seconds] × 30; 68°C for 5 minutes; 4°C overnight. After amplification, the PCR products (1118 bp) were analyzed by gel electrophoresis and purified via Qiaquick DNA extraction (Qiagen), and then cloned into pBS predigested with Eco RV. Following an overnight ligation, E. coli DH5α was transformed by the calcium chloride method and the colonies screened via the blue-white method using X-gal .
Cloning of rocF from strain G27 into pBS
The rocF gene was PCR-amplified as described above and cloned directly into pCR2.1 in E. coli strain Top10 by electroporation, according to manufacturer's guidelines (Invitrogen).
Sequencing of rocF genes
Plasmid DNA from white transformants was purified by Qiagen column chromatography and was digested with Cla I and Pst I restriction endonucleases to confirm presence of the insert. The rocF inserts were sequenced using T3 (forward primer; AATTAACCCTCACTAAAGGG) and T7-1 (reverse primer; GTAATACGACTCACTATAGGGC) by the Sanger dideoxynucleotide method at Iowa State University DNA Sequencing and Synthesis Facility. The sequence data have been deposited into the GenBank database as accession numbers EF126010 to EF126032.
Sequence and phylogenetic analysis
The sequences of the rocF gene of clinical isolates and laboratory-adapted strains were analyzed by BLAST searches, sequence alignments, and sequence translations at the National Center for Biotechnology Information website . Amino acid analyses of arginase proteins were carried out at the Expert Protein Analysis System Server . Multi-sequence analysis comparisons were conducted using CLUSTALW version 1.82 [62, 63] and files saved as *.aln, followed by importation into ClustalX . The neighbor-joining bootstrap algorithm with 111 generator seeds and 1000 trials was used to create a Phylip output file. The Phylip output file was used to draw the phylogenetic tree in TreeView version 1.6.6 [65, 66].
Site-directed mutagenesis of 26695 rocF
Plasmid pQE30-rocF, harboring the wild-type rocF gene from H. pylori strain 26695, was mutated using the Quik Change kit following the manufacturer's instructions (Stratagene, La Jolla, CA). The primer sequences were as follows: 1) I174M: DM141-RocFI174M-F1 5'GGAGGGTTAGAAATGGATCCTAAATGTTTG3'; DM142-RocFI174M-R1 5'CAAACATTTAGGATCCATTTCTAACCCTCC3' (Introduces extra Bam HI site, underlined); 2) S232I: DM143-RocFS232I-F1 5'GATATTATTTATCTCATTTTGGATTTGGAC3'; DM144-RocFS232I-R1 5'GTCCAAATCCAAAATGAGATAAATAATATC3';
3) D257N: DM266-D257NrocF-F1 5'GGCTGAGTTTTAATGAACTCAAGCAATTACTGG3'; DM267-D257NrocF-R1 5'CCAGTAATTGCTTGAGTTCATTAAAACTCAGCC3';
4) RocF-F6: gcggatcc ATGATTTTAGTAGGATTAGAAGCAGAG; Bam HI site underlined; non-rocF sequence in lower case); 5) RocF-R8: gcctgcag AGTAACTCCTTGCAAAAGA GTGCTTC; Pst I site underlined; non-rocF sequence in lower case). All constructs were confirmed by sequence analyses.
The University of South Alabama Medical Student Summer Research Program for support of JGH is appreciated. Thanks are given to R. Peek, N. Salama and B. Schneider for providing some of the H. pylori strains used in the study. We thank Harry Mobley for assistance with the urease measurements. The technical support of Katherine Horton is greatly appreciated. This work was supported by Public Health Service grant CA101931 (to DJM) from the National Institutes of Health, and the Australian Research Council (to GLM).
- Blaser MJ: Gastric Campylobacter-like organisms, gastritis, and peptic ulcer disease. Gastroenterology. 1987, 93 (2): 371-383.PubMedGoogle Scholar
- Blaser MJ: Helicobacter pylori and the pathogenesis of gastroduodenal inflammation. Journal of Infectious Diseases. 1990, 161 (4): 626-633.View ArticlePubMedGoogle Scholar
- Marshall BJ, McGechie DB, Rogers PA, Glancy RJ: Pyloric Campylobacter infection and gastroduodenal disease. Medical Journal of Australia. 1985, 142 (8): 439-444.PubMedGoogle Scholar
- Nomura A, Stemmermann GN, Chyou PH, Kato I, Perez-Perez GI, Blaser MJ: Helicobacter pylori infection and gastric carcinoma among Japanese Americans in Hawaii.[see comment]. New England Journal of Medicine. 1991, 325 (16): 1132-1136.View ArticlePubMedGoogle Scholar
- Parsonnet J, Friedman GD, Vandersteen DP, Chang Y, Vogelman JH, Orentreich N, Sibley RK: Helicobacter pylori infection and the risk of gastric carcinoma. N Engl J Med. 1991, 325 (16): 1127-1131.View ArticlePubMedGoogle Scholar
- Akopyanz N, Bukanov NO, Westblom TU, Berg DE: PCR-based RFLP analysis of DNA sequence diversity in the gastric pathogen Helicobacter pylori. Nucleic Acids Research. 1992, 20 (23): 6221-6225. 10.1093/nar/20.23.6221.PubMed CentralView ArticlePubMedGoogle Scholar
- Akopyanz N, Bukanov NO, Westblom TU, Kresovich S, Berg DE: DNA diversity among clinical isolates of Helicobacter pylori detected by PCR-based RAPD fingerprinting. Nucleic Acids Research. 1992, 20 (19): 5137-5142. 10.1093/nar/20.19.5137.PubMed CentralView ArticlePubMedGoogle Scholar
- Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ: Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature. 1999, 397 (6715): 176-180. 10.1038/16495.View ArticlePubMedGoogle Scholar
- Atherton JC, Cao P, Peek RM, Tummuru MK, Blaser MJ, Cover TL: Mosaicism in vacuolating cytotoxin alleles of Helicobacter pylori. Association of specific vacA types with cytotoxin production and peptic ulceration. J Biol Chem. 1995, 270 (30): 17771-17777. 10.1074/jbc.270.30.17771.View ArticlePubMedGoogle Scholar
- Censini S, Lange C, Xiang Z, Crabtree JE, Ghiara P, Borodovsky M, Rappuoli R, Covacci A: cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors. Proc Natl Acad Sci U S A. 1996, 93 (25): 14648-14653. 10.1073/pnas.93.25.14648.PubMed CentralView ArticlePubMedGoogle Scholar
- Foxall PA, Hu LT, Mobley HL: Use of polymerase chain reaction-amplified Helicobacter pylori urease structural genes for differentiation of isolates. Journal of Clinical Microbiology. 1992, 30 (3): 739-741.PubMed CentralPubMedGoogle Scholar
- Oudbier JH, Langenberg W, Rauws EA, Bruin-Mosch C: Genotypical variation of Campylobacter pylori from gastric mucosa. Journal of Clinical Microbiology. 1990, 28 (3): 559-565.PubMed CentralPubMedGoogle Scholar
- Salama N, Guillemin K, McDaniel TK, Sherlock G, Tompkins L, Falkow S: A whole-genome microarray reveals genetic diversity among Helicobacter pylori strains. Proc Natl Acad Sci U S A. 2000, 97 (26): 14668-14673. 10.1073/pnas.97.26.14668.PubMed CentralView ArticlePubMedGoogle Scholar
- Simor AE, Shames B, Drumm B, Sherman P, Low DE, Penner JL: Typing of Campylobacter pylori by bacterial DNA restriction endonuclease analysis and determination of plasmid profile. Journal of Clinical Microbiology. 1990, 28 (1): 83-86.PubMed CentralPubMedGoogle Scholar
- Cao P, Cover TL: Two different families of hopQ alleles in Helicobacter pylori. J Clin Microbiol. 2002, 40 (12): 4504-4511. 10.1128/JCM.40.12.4504-4511.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Tomasini ML, Zanussi S, Sozzi M, Tedeschi R, Basaglia G, De Paoli P: Heterogeneity of cag genotypes in Helicobacter pylori isolates from human biopsy specimens. J Clin Microbiol. 2003, 41 (3): 976-980. 10.1128/JCM.41.3.976-980.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- Colbeck JC, Hansen LM, Fong JM, Solnick JV: Genotypic profile of the outer membrane proteins BabA and BabB in clinical isolates of Helicobacter pylori. Infect Immun. 2006, 74 (7): 4375-4378. 10.1128/IAI.00485-06.PubMed CentralView ArticlePubMedGoogle Scholar
- Hennig EE, Allen JM, Cover TL: Multiple chromosomal loci for the babA gene in Helicobacter pylori. Infect Immun. 2006, 74 (5): 3046-3051. 10.1128/IAI.74.5.3046-3051.2006.PubMed CentralView ArticlePubMedGoogle Scholar
- Figueiredo C, Quint WG, Sanna R, Sablon E, Donahue JP, Xu Q, Miller GG, Peek RM, Blaser MJ, van Doorn LJ: Genetic organization and heterogeneity of the iceA locus of Helicobacter pylori. Gene. 2000, 246 (1-2): 59-68. 10.1016/S0378-1119(00)00054-8.View ArticlePubMedGoogle Scholar
- Go MF, Kapur V, Graham DY, Musser JM: Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure. Journal of Bacteriology. 1996, 178 (13): 3934-3938.PubMed CentralPubMedGoogle Scholar
- Logan RP, Berg DE: Genetic diversity of Helicobacter pylori.[erratum appears in Lancet 1997 Jan 4;349(9044):64]. Lancet. 1996, 348 (9040): 1462-1463. 10.1016/S0140-6736(05)65885-0.View ArticlePubMedGoogle Scholar
- Phadnis SH, Ilver D, Janzon L, Normark S, Westblom TU: Pathological significance and molecular characterization of the vacuolating toxin gene of Helicobacter pylori. Infection & Immunity. 1994, 62 (5): 1557-1565.Google Scholar
- Salaun L, Audibert C, Le Lay G, Burucoa C, Fauchere JL, Picard B: Panmictic structure of Helicobacter pylori demonstrated by the comparative study of six genetic markers. FEMS Microbiol Lett. 1998, 161 (2): 231-239.View ArticlePubMedGoogle Scholar
- Perales G, Sanchez J, Mohar A, Lara-Lemus R, Hernandez A, Herrera-Goepfert R, Barrios-Jacobo I, Ayala G: Single-step PCR amplification and enzyme restriction analysis of the entire Helicobacter pylori cytotoxin vacA gene for genetic variability studies. FEMS Microbiology Letters. 1999, 178 (1): 55-62. 10.1111/j.1574-6968.1999.tb13759.x.View ArticlePubMedGoogle Scholar
- Cover TL: The vacuolating cytotoxin of Helicobacter pylori. Mol Microbiol. 1996, 20 (2): 241-246. 10.1111/j.1365-2958.1996.tb02612.x.View ArticlePubMedGoogle Scholar
- Beji A, Vincent P, Darchis I, Husson MO, Cortot A, Leclerc H: Evidence of gastritis with several Helicobacter pylori strains. Lancet. 1989, 2 (8676): 1402-1403. 10.1016/S0140-6736(89)92020-5.View ArticlePubMedGoogle Scholar
- Kuipers EJ, Israel DA, Kusters JG, Gerrits MM, Weel J, van Der Ende A, van Der Hulst RW, Wirth HP, Hook-Nikanne J, Thompson SA, Blaser MJ: Quasispecies development of Helicobacter pylori observed in paired isolates obtained years apart from the same host. J Infect Dis. 2000, 181 (1): 273-282. 10.1086/315173.PubMed CentralView ArticlePubMedGoogle Scholar
- Israel DA, Salama N, Krishna U, Rieger UM, Atherton JC, Falkow S, Peek RM: Helicobacter pylori genetic diversity within the gastric niche of a single human host. Proc Natl Acad Sci U S A. 2001, 98 (25): 14625-14630. 10.1073/pnas.251551698.PubMed CentralView ArticlePubMedGoogle Scholar
- McGee DJ, Mobley HL: Mechanisms of Helicobacter pylori infection: bacterial factors. Curr Top Microbiol Immunol. 1999, 241: 155-180.PubMedGoogle Scholar
- Marshall BJ, Barrett LJ, Prakash C, McCallum RW, Guerrant RL: Urea protects Helicobacter (Campylobacter) pylori from the bactericidal effect of acid. Gastroenterology. 1990, 99 (3): 697-702.PubMedGoogle Scholar
- Mobley HL: The role of Helicobacter pylori urease in the pathogenesis of gastritis and peptic ulceration. Alimentary Pharmacology & Therapeutics. 1996, 10 Suppl 1: 57-64.View ArticleGoogle Scholar
- Eaton KA, Brooks CL, Morgan DR, Krakowka S: Essential role of urease in pathogenesis of gastritis induced by Helicobacter pylori in gnotobiotic piglets. Infect Immun. 1991, 59 (7): 2470-2475.PubMed CentralPubMedGoogle Scholar
- Eaton KA, Krakowka S: Effect of gastric pH on urease-dependent colonization of gnotobiotic piglets by Helicobacter pylori. Infect Immun. 1994, 62 (9): 3604-3607.PubMed CentralPubMedGoogle Scholar
- Akada JK, Shirai M, Takeuchi H, Tsuda M, Nakazawa T: Identification of the urease operon in Helicobacter pylori and its control by mRNA decay in response to pH. Mol Microbiol. 2000, 36 (5): 1071-1084. 10.1046/j.1365-2958.2000.01918.x.View ArticlePubMedGoogle Scholar
- McGee DJ, Radcliff FJ, Mendz GL, Ferrero RL, Mobley HL: Helicobacter pylori rocF is required for arginase activity and acid protection in vitro but is not essential for colonization of mice or for urease activity. J Bacteriol. 1999, 181 (23): 7314-7322.PubMed CentralPubMedGoogle Scholar
- Mendz GL, Hazell SL: The urea cycle of Helicobacter pylori. Microbiology. 1996, 142 ( Pt 10): 2959-2967.View ArticleGoogle Scholar
- Mendz GL, Holmes EM, Ferrero RL: In situ characterization of Helicobacter pylori arginase. Biochim Biophys Acta. 1998, 1388 (2): 465-477.View ArticlePubMedGoogle Scholar
- Mendz GL, Hazell SL: Aminoacid utilization by Helicobacter pylori. Int J Biochem Cell Biol. 1995, 27 (10): 1085-1093. 10.1016/1357-2725(95)00069-2.View ArticlePubMedGoogle Scholar
- Gobert AP, McGee DJ, Akhtar M, Mendz GL, Newton JC, Cheng Y, Mobley HL, Wilson KT: Helicobacter pylori arginase inhibits nitric oxide production by eukaryotic cells: a strategy for bacterial survival. Proc Natl Acad Sci U S A. 2001, 98 (24): 13844-13849. 10.1073/pnas.241443798.PubMed CentralView ArticlePubMedGoogle Scholar
- Zabaleta J, McGee DJ, Zea AH, Hernandez CP, Rodriguez PC, Sierra RA, Correa P, Ochoa AC: Helicobacter pylori arginase inhibits T cell proliferation and reduces the expression of the TCR z-chain (CD3z). J Immunol. 2004, 173 (1): 586-593.View ArticlePubMedGoogle Scholar
- Dunn BE, Campbell GP, Perez-Perez GI, Blaser MJ: Purification and characterization of urease from Helicobacter pylori. Journal of Biological Chemistry. 1990, 265 (16): 9464-9469.PubMedGoogle Scholar
- Ferrero RL, Hazell SL, Lee A: The urease enzymes of Campylobacter pylori and a related bacterium. Journal of Medical Microbiology. 1988, 27 (1): 33-40.View ArticlePubMedGoogle Scholar
- McGee DJ, Zabaleta J, Viator RJ, Testerman TL, Ochoa AC, Mendz GL: Purification and characterization of Helicobacter pylori arginase, RocF: unique features among the arginase superfamily. Eur J Biochem. 2004, 271 (10): 1952-1962. 10.1111/j.1432-1033.2004.04105.x.View ArticlePubMedGoogle Scholar
- Langford ML, Zabaleta J, Ochoa AC, Testerman TL, McGee DJ: In Vitro and In Vivo Complementation of the Helicobacter pylori Arginase Mutant Using an Intergenic Chromosomal Site. Helicobacter. 2006, 11 (5): 477-493. 10.1111/j.1523-5378.2006.00441.x.PubMed CentralView ArticlePubMedGoogle Scholar
- Oh JD, Kling-Backhed H, Giannakis M, Xu J, Fulton RS, Fulton LA, Cordum HS, Wang C, Elliott G, Edwards J, Mardis ER, Engstrand LG, Gordon JI: The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression. Proc Natl Acad Sci U S A. 2006, 103 (26): 9999-10004. 10.1073/pnas.0603784103.PubMed CentralView ArticlePubMedGoogle Scholar
- Eppinger M, Baar C, Linz B, Raddatz G, Lanz C, Keller H, Morelli G, Gressmann H, Achtman M, Schuster SC: Who ate whom? Adaptive Helicobacter genomic changes that accompanied a host jump from early humans to large felines. PLoS Genet. 2006, 2 (7): e120-10.1371/journal.pgen.0020120.PubMed CentralView ArticlePubMedGoogle Scholar
- Reynolds DJ, Penn CW: Characteristics of Helicobacter pylori growth in a defined medium and determination of its amino acid requirements. Microbiology. 1994, 140 ( Pt 10): 2649-2656.View ArticleGoogle Scholar
- Testerman TL, Conn PB, Mobley HL, McGee DJ: Nutritional requirements and antibiotic resistance patterns of Helicobacter species in chemically defined media. J Clin Microbiol. 2006, 44 (5): 1650-1658. 10.1128/JCM.44.5.1650-1658.2006.PubMed CentralView ArticlePubMedGoogle Scholar
- Testerman TL, McGee DJ, Mobley HL: Helicobacter pylori growth and urease detection in the chemically defined medium Ham's F-12 nutrient mixture. J Clin Microbiol. 2001, 39 (11): 3842-3850. 10.1128/JCM.39.11.3842-3850.2001.PubMed CentralView ArticlePubMedGoogle Scholar
- Suerbaum S, Smith JM, Bapumia K, Morelli G, Smith NH, Kunstmann E, Dyrek I, Achtman M: Free recombination within Helicobacter pylori. Proc Natl Acad Sci U S A. 1998, 95 (21): 12619-12624. 10.1073/pnas.95.21.12619.PubMed CentralView ArticlePubMedGoogle Scholar
- Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC: The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997, 388 (6642): 539-547. 10.1038/41483.View ArticlePubMedGoogle Scholar
- Hennig EE, Mernaugh R, Edl J, Cao P, Cover TL: Heterogeneity among Helicobacter pylori strains in expression of the outer membrane protein BabA. Infect Immun. 2004, 72 (6): 3429-3435. 10.1128/IAI.72.6.3429-3435.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Naito M, Yamazaki T, Tsutsumi R, Higashi H, Onoe K, Yamazaki S, Azuma T, Hatakeyama M: Influence of EPIYA-repeat polymorphism on the phosphorylation-dependent biological activity of Helicobacter pylori CagA. Gastroenterology. 2006, 130 (4): 1181-1190. 10.1053/j.gastro.2005.12.038.View ArticlePubMedGoogle Scholar
- van Doorn LJ, Figueiredo C, Sanna R, Blaser MJ, Quint WG: Distinct variants of Helicobacter pylori cagA are associated with vacA subtypes. J Clin Microbiol. 1999, 37 (7): 2306-2311.PubMed CentralPubMedGoogle Scholar
- Pflock M, Finsterer N, Joseph B, Mollenkopf H, Meyer TF, Beier D: Characterization of the ArsRS regulon of Helicobacter pylori, involved in acid adaptation. Journal of Bacteriology. 2006, 188 (10): 3449-3462. 10.1128/JB.188.10.3449-3462.2006.PubMed CentralView ArticlePubMedGoogle Scholar
- Wen Y, Marcus EA, Matrubutham U, Gleeson MA, Scott DR, Sachs G: Acid-adaptive genes of Helicobacter pylori. Infect Immun. 2003, 71 (10): 5921-5939. 10.1128/IAI.71.10.5921-5939.2003.PubMed CentralView ArticlePubMedGoogle Scholar
- McGee DJ, Coker C, Testerman TL, Harro JM, Gibson SV, Mobley HL: The Helicobacter pylori flbA flagellar biosynthesis and regulatory gene is required for motility and virulence and modulates urease of H. pylori and Proteus mirabilis. J Med Microbiol. 2002, 51 (11): 958-970.View ArticlePubMedGoogle Scholar
- McGee DJ, May CA, Garner RM, Himpsl JM, Mobley HL: Isolation of Helicobacter pylori genes that modulate urease activity. J Bacteriol. 1999, 181 (8): 2477-2484.PubMed CentralPubMedGoogle Scholar
- Sambrook J: Molecular Cloning: A Laboratory Manual. Edited by: Laboratory. CSH. 1989, Cold Spring Harbor, N. Y. , 2ndGoogle Scholar
- National Center for Biotechnology Information.http://www.ncbi.nlm.nih.gov
- ExPASy Proteomics Server.http://us.expasy.org
- Thompson JD: CLUSTAL W: improving thesensitivity of progressive multiple sequence alignment through sequenceweighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research. 1994, 22: 4673-4680. 10.1093/nar/22.22.4673.PubMed CentralView ArticlePubMedGoogle Scholar
- European Bioinformatics Institute: ClustalW.http://www.ebi.ac.uk/clustalw/
- Thompson JD: The ClustalX windows interface: flexible strategies for multiple sequencealignment aided by quality analysis tools. Nucleic Acids Research. 1997, 24: 4876-4882. 10.1093/nar/25.24.4876.View ArticleGoogle Scholar
- Rod Page's Home Page. http://taxonomy.zoology.gla.ac.uk/rod/rod.html
- Page RDM: TREEVIEW: An application to display phylogenetic trees on personal computers. Computer Applications in the Biosciences. 1996, 12: 357-358.PubMedGoogle Scholar
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