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Infection and Immunity, February 2004, p. 766-773, Vol. 72, No. 2
0019-9567/04/$08.00+0 DOI: 10.1128/IAI.72.2.766-773.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Acid-Responsive Gene Induction of Ammonia-Producing Enzymes in Helicobacter pylori Is Mediated via a Metal-Responsive Repressor Cascade
Arnoud H. M. van Vliet,* Ernst J. Kuipers, Jeroen Stoof, Sophie W. Poppelaars, and Johannes G. Kusters
Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
Received 29 September 2003/
Accepted 15 October 2003

ABSTRACT
Although the adaptive mechanisms allowing the gastric pathogen
Helicobacter pylori to survive acid shocks have been well documented,
the mechanisms allowing growth at mildly acidic conditions (pH

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 NiCl
2 resulted in a similar induction of urease activity
(at low NiCl
2 concentration) and amidase activity (at

500
µM NiCl
2) 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
Helicobacter pylori is an important human pathogen, which colonizes
the mucus layer overlaying the gastric epithelium. Colonization
with
H. pylori results in chronic gastric mucosal inflammation,
which can progress to peptic ulcer disease and gastric carcinomas
(
16). The pH in the gastric mucus layer is thought to vary between
4 and 6.5, with occasional acid shocks of pH <2 occurring
when the mucus layer is damaged. Since
H. pylori demonstrates
optimal growth at neutral pH, survival and growth of
H. pylori in the hostile environment of the stomach require mechanisms
to survive acid shocks and allow growth at mildly acidic pH
(
31,
35). Resistance of
H. pylori to acid shocks requires production
of ammonia by urease-mediated degradation of urea (summarized
in reference
35).
H. pylori produces large amounts of urease,
up to 10% of its total protein content, and expression of urease
is controlled at the transcriptional, posttranscriptional, and
posttranslational level (
1,
31,
38,
39). Cytoplasmic urease
activity is under strict pH-mediated control, since the intracellular
urea concentration is controlled by the H
+-gated urea transporter
UreI (
10,
30,
42).
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
Bacterial strains, plasmids, media, and growth conditions.
H. pylori wild-type strain 26695 (
37) and its isogenic
fur (
8),
nikR (
39), and
nikR fur (the present study) mutants were routinely
cultured on Dent agar, consisting of Columbia agar supplemented
with 7% saponin-lysed horse blood, 0.004% triphenyltetrazolium
chloride (Sigma, St. Louis, Mo.), and Dent selective supplement
(Oxoid, Basingstoke, United Kingdom) at 37°C under microaerophilic
conditions (10% CO
2, 5% O
2, and 85% N
2). Broth cultures were
grown in brucella broth (Difco, Sparks, Md.) supplemented with
either 0.2% ß-cyclodextrins (Fluka, Buchs, Switzerland)
(BBC) or 3% newborn calf serum (Gibco/Life Technologies, Breda,
The Netherlands) (BBN). NiCl
2 was purchased from Sigma, filter
sterilized, and used at the indicated concentrations (
38,
39).
The pH of broth medium was adjusted to 5.5 by using HCl as described
previously (
8) and did not change by more than 0.5 pH during
growth experiments or by NiCl
2 supplementation. For antibiotic
selection, growth media were supplemented with kanamycin or
chloramphenicol to final concentrations of 20 or 10 µg/ml,
respectively.
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).
Urease, amidase, and formamidase enzyme assays.
The enzymatic activity of urease, amidase, and formamidase were
determined in fresh
H. pylori lysates by measuring ammonia production
from hydrolysis of urea, acrylamide, or formamide, respectively,
by using the Berthelot reaction as described previously (
40).
The concentration of ammonia in the samples was inferred from
a standard NH
4Cl concentration curve. Enzyme activity was expressed
as micromoles of substrate hydrolyzed per minute per milligram
of protein.
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
Transcription and activity of H. pylori ammonia-producing enzymes is induced at pH 5.5.
The effect of growth in acidic conditions on the activity of
the three main ammonia-producing enzymes of the reference
H. pylori strain 26695 was quantitated after overnight growth at
pH 7.0 and pH 5.5. The latter pH was chosen to represent the
average conditions thought to occur in the gastric mucus layer,
and it also is the lower limit at which most
H. pylori strains
still grow in vitro (
6,
8). When compared to enzyme activity
at pH 7.0, growth at pH 5.5 resulted in a significant increase
in urease, amidase, and formamidase activity (Fig.
1A to C).
The increases were approximately fourfold for urease, ninefold
for amidase, and fivefold for formamidase and were similar in
ß-cyclodextrin- and serum-supplemented media, thus
excluding the effect of medium additives (not shown). There
was no increase in urease, amidase, and formamidase activity
when the medium was first adjusted to pH 5.5 and then subsequently
readjusted to pH 7.0, excluding the possible artifact that the
induction of enzyme activity was mediated by precipitation of
medium components (not shown).
The increase in enzyme activity was mediated by increased transcription
of each of the genes, as tested by Northern hybridization (Fig.
1D). The increase in the two
ureAB transcripts (
1) was relatively
minor and suggests that a major part of the induction in urease
activity is mediated through activation of inactive urease apoenzyme
(
30,
31,
39). In contrast, the relative increase in the
amiE and
amiF transcripts after growth in acidic conditions was much
more pronounced compared to
ureAB transcription (Fig.
1D) and
is likely to be mostly mediated via increased transcription
of the amidase and formamidase genes. Transcription of the
hspA (HP0011) chaperone-encoding gene was included as an example
of a pH-independently transcribed gene and excludes the possibility
that the observed acid-responsive changes in
ureA,
amiE, and
amiF transcription are caused by global changes in transcriptional
activity.
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).
The nikR and fur gene products govern acid-responsive gene regulation in H. pylori.
The
H. pylori genome contains two genes encoding regulatory
proteins known to be involved in urease, amidase, and formamidase
regulation: the HP1027 (
fur) gene encoding the Fur regulator,
which mediates iron-responsive regulation of both amidases (
40),
and the HP1338 (
nikR) gene encoding the NikR regulator, which
mediates nickel-responsive induction of urease (
12,
39). Isogenic
fur and
nikR mutants, as well as a
nikR fur double mutant, were
used to investigate the role of the Fur and NikR proteins in
acid-responsive induction of the urease, amidase, and formamidase
enzymes (Fig.
3). Amidase and formamidase activity was constitutively
high in the
fur and
nikR fur double mutants and was not further
induced at acidic pH (Fig.
3B and C). In contrast, the
fur mutation
did not affect urease activity at either pH (Fig.
3A). Conversely,
mutation of the
nikR gene did not affect the activity of any
of the three enzymes at pH 7.0 but had a significant effect
on the acid-responsive induction of amidase and formamidase
(Fig.
3B and C). The
nikR mutant also displayed lowered acid-responsive
induction of urease activity, albeit not statistically significant
(Fig.
3A). This is similar to the effect of the
nikR mutation
on nickel-responsive induction of urease expression reported
previously (
39). The induction still present is probably due
to increased activation of urease apoenzyme, as suggested previously
(
30,
31,
39). The effect of the
nikR mutation on acid-responsive
induction of amidase and formamidase activity was similar, since
the
nikR mutant was unable to induce enzyme activity at pH 5.5
to the levels found in the wild-type strain (Fig.
3B and C).
The
nikR fur double mutant displayed a phenotype similar to
the
nikR mutant with regard to urease activity and induction
(Fig.
3A) but was virtually identical to the
fur mutant with
regard to amidase and formamidase activity and induction (Fig.
3B and C).
Acid-responsive transcriptional regulation is mediated by a repressor cascade.
The inverse effects of the
nikR and
fur mutations on expression
of ammonia-producing enzymes indicated interaction or overlap
between the two regulatory systems. Therefore, we investigated
the effect of medium acidification on the transcription of
fur and
nikR genes themselves (Fig.
4). The
fur gene displayed acid-
responsive repression of transcription (Fig.
4B), as described
previously (
8). In contrast, transcription of the
nikR gene
was induced by medium acidification (Fig.
4B). The
nikR transcript
was relatively unstable, resulting in partial degradation of
the
nikR mRNA on Northern hybridization (Fig.
4B). Mutation
of the
nikR gene had a profound effect on the transcription
of the
fur gene, which was significantly increased in the
nikR mutant, indicating that NikR represses
fur transcription (Fig.
4C) (
12). There was, however, no discernible effect of the
fur mutation on
nikR transcription (not shown), indicating that
the NikR regulator is hierarchically higher ranked than the
Fur regulator in the response to environmental acidification.

DISCUSSION
The ability to survive and adapt to the hostile environmental
conditions within the mammalian host is a hallmark of successful
pathogens. Adaptation to such conditions is mostly mediated
at the transcriptional level via regulation of transcription,
but alternative approaches such as differential mRNA processing,
phase variation, posttranslational protein modification, and
genetic reshuffling are all known to play important roles as
adaptive response mechanisms in pathogenic microorganisms. The
human gastric pathogen
H. pylori is unique among pathogens,
since it is known to utilize all of these methods (
13).
H. pylori is the sole colonizer of an ecological niche which is hostile
with respect to environmental pH, inflammatory response, and
availability of nutrients and is extraordinarily adapted to
the conditions occurring in the human stomach. Here part of
the regulatory mechanisms allowing
H. pylori to respond to mildly
acidic growth conditions by increasing the expression of three
of its ammonia-producing enzymes are described.
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.

ACKNOWLEDGMENTS
We thank Angela Heijens for technical assistance and Florian
D. Ernst for helpful discussions.

FOOTNOTES
* Corresponding author. Mailing address: Department of Gastroenterology and Hepatology, Erasmus MC-University Medical Center, Room L-459, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands. Phone: 31-10-4635944. Fax: 31-10-4632793. E-mail:
a.h.m.vanvliet{at}erasmusmc.nl.

Editor: V. J. DiRita

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Infection and Immunity, February 2004, p. 766-773, Vol. 72, No. 2
0019-9567/04/$08.00+0 DOI: 10.1128/IAI.72.2.766-773.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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