Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
Received 29 September 2003/ Accepted 15 October 2003
| ABSTRACT |
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5.5) are still poorly understood. Here we demonstrate that H. pylori strain 26695 increases the transcription and activity of its urease, amidase, and formamidase enzymes four- to ninefold in response to growth at pH 5.5. Supplementation of growth medium with NiCl2 resulted in a similar induction of urease activity (at low NiCl2 concentration) and amidase activity (at
500 µM NiCl2) but did not affect formamidase activity. Mutation of the fur gene, which encodes an iron-responsive repressor of both amidases, resulted in a constitutively high level of amidase and formamidase activity at either pH but did not affect urease activity at pH 7.0 or pH 5.5. In contrast, mutation of the nikR gene, encoding the nickel-responsive activator of urease expression, resulted in a significant reduction of acid-responsive induction of amidase and formamidase activity. Finally, acid-responsive repression of fur transcription was absent in the H. pylori nikR mutant, whereas transcription of the nikR gene itself was increased at pH 5.5 in wild-type H. pylori. We hypothesize that H. pylori uses a repressor cascade to respond to low pH, with NikR initiating the response directly via the urease operon and indirectly via the members of the Fur regulon. | INTRODUCTION |
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In contrast to the mechanisms involved in the resistance to acid shocks, relatively little is known about the mechanisms, allowing growth at mildly acidic conditions (pH
5.5). The chronicity of colonization, however, suggests that H. pylori is able to grow at mildly acidic pH. Growth at acidic pH induces changes in lipopolysaccharide composition (23, 26, 36), increases expression of chaperone-like proteins (19), and affects expression of several genes at the transcriptional and protein expression level (4-6, 15, 24, 25, 34, 43). However, the exact role in acid resistance of many of these factors is largely unknown.
There is a close link between metal metabolism and acid resistance in H. pylori. Transcription of the urease structural genes, as well as the acid-activated enzyme activity of H. pylori urease, is dependent on the availability of the nickel cofactor (31, 38), probably via the NikR nickel-responsive regulatory protein (12, 39). In addition, the iron-responsive regulator Fur is required for growth at pH 5.5 (8). The relationship between the NikR and Fur metal-regulatory systems and acid resistance may not solely depend on a disturbed metal homeostasis, since we demonstrated recently that Fur mediates iron-responsive regulation of the H. pylori paralogous amidases AmiE and AmiF (40). Both amidases degrade amide substrates to ammonia and the corresponding carboxylic acid and, together with the amino acid deaminases, they probably represent alternative systems for ammonia production in times of urea shortage (9, 22, 25, 32, 33, 40). Recent studies using transcriptome analyses have provided evidence for acid-responsive regulation of diverse ammonia-generating pathways (25, 43), but thus far the responsible regulatory systems mediating this acid-responsive regulation were not described.
Based on our previous observations about the roles of the NikR and Fur proteins in the regulation of ammonia-producing enzymes (12, 38-40), we hypothesized that NikR and Fur may be two important mediators of acid-responsive gene regulation in H. pylori. Therefore, the effect of growth in mild acidic conditions on transcription and activity of the three main H. pylori enzymes involved in ammonia production was analyzed, and it was observed that transcription and the activity of all three enzymes is significantly induced upon acidification. Subsequently, it was shown that both NikR and Fur are responsible for the observed acid-responsive regulation of urease, amidase, and formamidase activity, and we present here a model wherein a cascade of two or more regulatory proteins is enough to mediate adaptation to acidic conditions.
| MATERIALS AND METHODS |
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RNA hybridization. RNA was isolated by using TRIzol (Invitrogen, Carlsbad, Calif.) according to the manufacturer's instructions, separated on 2% formaldehyde-1.5% agarose gels in 20 mM sodium phosphate buffer, and subsequently transferred to nylon membranes (Roche, Basel, Switzerland) by using standard protocols (38). After transfer, RNA was covalently bound to the membrane by cross-linking with 0.120 J of UV light (254-nm wavelength)/cm2. Transferred RNA was visualized by methylene blue staining, and RNA samples were normalized based on 16S and 23S rRNA band intensities as described previously (38, 41).
Internal fragments of the ureA, amiE, amiF, hspA, fur, and nikR genes were PCR amplified from genomic DNA of H. pylori 26695 with the primers listed in Table 1. The resulting PCR fragments contained a T7 promoter sequence on the noncoding strand and were used for the production of antisense RNA probes labeled with digoxigenin (DIG) by in vitro transcription with T7 RNA polymerase (Roche). Northern hybridization and stringency washes were performed at 68°C, and bound probe was visualized with the DIG detection kit (Roche) and the chemiluminescent substrate CPD-Star (Amersham Pharmacia) (38). The sizes of hybridizing mRNA species were determined by comparison with the DIG-labeled RNA Molecular Weight Marker I (Roche).
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Recombinant DNA techniques. Restriction enzymes and DNA-modifying enzymes were purchased from Promega (Madison, Wis.), and standard protocols were used for the manipulation of DNA and the transformation of H. pylori (7). PCR was carried out with Taq polymerase (Promega). The H. pylori 26695 nikR fur double mutant was constructed by natural transformation of the H. pylori 26695 fur mutant with plasmid pAV364 as described previously (39). Correct replacement of the nikR gene by the interrupted version was confirmed by using PCR (39).
| RESULTS |
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Nickel supplementation of growth media mimicks acidification.
To further define the link between nickel and acid, we investigated the effect of nickel supplementation on urease, amidase, and formamidase activity. When H. pylori strain 26695 was grown in media of pH 7.0 supplemented with NiCl2 to final concentrations ranging from 1 to 1,000 µM, urease activity was already induced at low concentrations of NiCl2 to levels similar to activity at pH 5.5 (Fig. 2A), a finding consistent with earlier reports (12, 38, 39). In contrast, amidase and formamidase activity was not affected by low concentrations of NiCl2 (Fig. 2B,C). However, at NiCl2 concentrations of 500 µM and higher, amidase activity increased significantly (Fig. 2B), while formamidase activity was not affected (Fig. 2C). The level of amidase activity at NiCl2 concentrations of
500 µM was similar to that observed with unsupplemented growth media adjusted to pH 5.5 (Fig. 1B).
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| DISCUSSION |
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Acidic pH is probably the most important environmental stress for H. pylori, which it encounters both during the initial and the chronic phase of colonization (35). Initial colonization requires protection against short-term acid exposure in the lumen of the stomach, where the pH is usually <2. Once established, H. pylori is present in the gastric mucus layer, where the average pH is
5.5 (27, 29). Despite its small genome size of 1.7 Mbp (3, 37), H. pylori is able to survive both these short-term low pH shocks and long-term exposure to mildly acidic conditions without being a truely acidophilic organism.
The urease enzyme mediates resistance of H. pylori to acid shocks via hydrolysis of urea to form ammonia, with subsequent buffering of either the periplasm or cytoplasm of H. pylori (28, 35). This short-term response to acid also requires acid-activated urea import via UreI and acid activation of urease apoenzyme via increased nickel availability (31, 42). In contrast, the long-term H. pylori response to acidic conditions is multifactorial, leading to modifications in membrane composition and H. pylori metabolism (4-6, 15, 19, 23-26, 34, 36, 43). Here it is demonstrated that growth at acidic conditions results in increased transcription and activity of the ammonia-producing enzymes urease, amidase, and formamidase and that part of this response is mediated via a regulatory cascade consisting of the NikR and Fur metal-regulatory proteins of H. pylori. In two recent studies on acid-responsive transcriptome analyses, it was also reported that several genes encoding for ammonia-producing enzymes were induced by medium acidification, and these included the ureAB, amiE, and amiF genes (25, 43). However, these findings were not further confirmed on the enzyme activity level, nor were the regulatory systems mediating the response identified. Many of the genes identified as acid regulated in these recent studies may well be regulated via either the NikR or Fur regulators but, again, this requires experimental validation.
The connection between pH and metal bioavailability in bacterial pathogens has been well established for iron, since a low pH stabilizes the readily oxidated ferrous form of iron. However, whereas iron plays an important role in H. pylori gene regulation, its role in acid resistance has been less clear. The iron-responsive regulator Fur is required for acid resistance, but this phenotype was reported to be independent of its role in iron regulation (8). Together with the previously reported role of Fur in regulation of the H. pylori amidases (40), this suggests that mutation of the fur gene disturbs the response to acidification either by constitutive overexpression of amidase or via another regulatory function not yet identified.
In H. pylori, the main link between metals and acid resistance is nickel. Nickel is cofactor of the urease enzyme, which is absolutely essential for acid survival of H. pylori. Urease expression and activity is regulated via nickel availability by the NikR regulatory protein (12, 31, 38, 39). The H. pylori NikR protein is a homolog of the Escherichia coli NikR protein, which regulates nickel acquisition via the Nik ABC transporter (11, 14). In H. pylori, the acquisition of nickel is required in the induction of urease activity (but not transcription) upon acid shock (31) and is likely to play a role in the transcriptional induction of urease upon growth in acidic conditions described here. Interestingly, mutation of the nikR gene resulted only in a small decrease in urease activity, which was not statistically significant (Fig. 3A). This is probably due to the NikR-independent activation of inactive urease apoenzyme previously described (31, 39), which masks the effect of the nikR mutation as shown previously for the effect of low concentrations of NiCl2 (39).
NikR also plays a role in regulation of nickel uptake in H. pylori (12) and, as such, the NikR protein can mediate regulation of several necessary processes for ammonia production in H. pylori: (i) induction of urease expression in acidic conditions (the present study) (30, 31) or nickel-rich (12, 38, 39) conditions and (ii) indirect regulation of amidase via regulation of the fur gene (the present study). Identification of additional targets for the NikR regulatory system via transcriptional profiling should allow for the identification of alternative or additional roles of NikR in acid resistance or ammonia production by H. pylori, as has been done recently for the identification of acid-responsive genes in H. pylori (2, 4, 15, 25, 43).
The NikR and Fur proteins generally function as transcriptional repressor proteins through binding of operators in their target promoters, blocking access of RNA polymerase, and subsequent transcription (11, 17). The repressor cascade of NikR and Fur described in the present study adds another level of complexity to this model. We hypothesize that the NikR protein ranks higher in the hierarchy, since NikR regulates fur transcription (Fig. 5) (12), whereas the reverse regulation does not occur (not shown). This view is also supported by the phenotypes of a H. pylori nikR fur double mutant (Fig. 3), which resembled the nikR mutant with regard to urease activity but resembled the fur mutant with regard to amidase and formamidase activity. A putative role for NikR as master regulator for acid-responsive regulation is also supported by the role of nickel in acid resistance of H. pylori (12, 31, 38, 39). The regulatory cascade proposed here utilizes two repressors each only allowing on/off regulation but, by varying the levels of Fur protein in cells, NikR not only regulates expression of its own regulon but also mediates changes in all members of the Fur regulon indirectly via regulation of fur transcription (Fig. 5). Since the effect of Fur on formamidase is indirect (40), it is likely that there is a third, as-yet-unknown regulator involved that ranks hierarchically below Fur (Fig. 5). These added levels of complexity should allow for the fine-tuning of the response to acid and possibly other relevant stresses. Other regulatory systems may also communicate or interact with the NikR or Fur regulons (12, 18, 20, 21, 25), since such intensive regulatory cross talk may allow H. pylori to mount protective responses to a multitude of different stresses despite a paucity of regulatory systems. In conclusion, H. pylori displays acid-responsive induction of its ammonia-producing enzymes at the transcriptional level via a regulatory cascade which contains the NikR and Fur repressor proteins (Fig. 5). The characterization of the Fur and NikR regulons may provide further insight in the mechanisms allowing H. pylori to persistently colonize the gastric environment.
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| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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