Journal of Bacteriology, May 2000, p. 2716-2724, Vol. 182, No. 10
0021-9193/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

Institut für Biologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
Received 25 October 1999/Accepted 21 February 2000
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ABSTRACT |
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Two energy-generating hydrogenases enable the aerobic hydrogen bacterium Ralstonia eutropha (formerly Alcaligenes eutrophus) to use molecular hydrogen as the sole energy source. The complex synthesis of the nickel-iron-containing enzymes has to be efficiently regulated in response to H2, which is available in low amounts in aerobic environments. H2 sensing in R. eutropha is achieved by a hydrogenase-like protein which controls the hydrogenase gene expression in concert with a two-component regulatory system. In this study we show that the H2 sensor of R. eutropha is a cytoplasmic protein. Although capable of H2 oxidation with redox dyes as electron acceptors, the protein did not support lithoautotrophic growth in the absence of the energy-generating hydrogenases. A specifically designed overexpression system for R. eutropha provided the basis for identifying the H2 sensor as a nickel-containing regulatory protein. The data support previous results which showed that the sensor has an active site similar to that of prototypic [NiFe] hydrogenases (A. J. Pierik, M. Schmelz, O. Lenz, B. Friedrich, and S. P. J. Albracht, FEBS Lett. 438:231-235, 1998). It is demonstrated that in addition to the enzymatic activity the regulatory function of the H2 sensor is nickel dependent. The results suggest that H2 sensing requires an active [NiFe] hydrogenase, leaving the question open whether only H2 binding or subsequent H2 oxidation and electron transfer processes are necessary for signaling. The regulatory role of the H2-sensing hydrogenase of R. eutropha, which has also been investigated in other hydrogen-oxidizing bacteria, is intimately correlated with a set of typical structural features. Thus, the family of H2 sensors represents a novel subclass of [NiFe] hydrogenases denoted as the "regulatory hydrogenases."
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INTRODUCTION |
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Molecular hydrogen is frequently
used as an energy source by diverse prokaryotic organisms. Many of
these bacterial and archaeal species harbor multiple hydrogenases which
mediate heterolytic cleavage of H2 into 2 H+
and 2 e
. [NiFe] hydrogenases are the most dominant
enzymes, representing a fairly conserved family of proteins, composed
of at least a large active site-containing subunit and a small
electron-transferring subunit which bears one to three FeS clusters
(1, 2, 18).
The facultative chemolithoautotrophic proteobacterium Ralstonia eutropha H16 (formerly Alcaligenes eutrophus [7]) harbors two energy-generating [NiFe] hydrogenases, a membrane-bound enzyme (MBH) and a cytoplasmic enzyme (SH). The MBH is primarily involved in electron transport-coupled phosphorylation, whereas the SH is able to reduce NAD and thus provides the cell with reducing equivalents (38, 40). The composition of the MBH resembles the prototype of [NiFe] hydrogenases whose atomic structure has been resolved by X-ray analysis (50). The two subunits of the R. eutropha MBH, encoded by hoxK and hoxG, are anchored to the outer face of the cytoplasmic membrane via a b-type cytochrome (4). The SH, encoded by hoxF, hoxU, hoxY, and hoxH, contains an FeS-flavoprotein in addition to the hydrogenase moiety (30). Mutants disrupted in either one of the two hydrogenases maintain their ability to grow on H2, which indicates that the two enzymes can replace each other physiologically (23).
The hydrogenase-related genes of R. eutropha are organized in the MBH and the SH operons, which are regulated coordinately (42). The MBH operon comprises 10 MBH-specific genes in addition to a set of accessory genes whose products are involved in the complex posttranslational maturation of the hydrogenases and the regulation of both the MBH and the SH operon (5, 11, 24, 41). The SH operon harbors the structural genes of the NAD-reducing hydrogenase together with a set of accessory genes which code for maturation proteins (45, 47, 52).
Hydrogenase gene expression is controlled by the major transcription
factor HoxA, a member of the NtrC family of response regulators
(12). HoxA binds specifically at the upstream regions of the
MBH and SH operons and activates transcription in concert with the
54-containing RNA polymerase (42, 54).
Transcription activation by HoxA is stimulated by at least two
environmental signals: the presence of molecular hydrogen and/or
limitation of organic carbon and energy sources (25, 42).
Recognition of molecular hydrogen by cells of R. eutropha is
mediated by a complex signal transduction system consisting of the
proteins HoxB and HoxC which share features of [NiFe] hydrogenases,
and HoxJ, a histidine protein kinase which has autophosphorylation
capacity with ATP as the phosphoryl donor (25, 26).
Deletions in hoxB or hoxC of R. eutropha prevent hydrogenase from being synthesized, whereas a
knockout of hoxJ leads to H2-independent
high-level hydrogenase gene expression. The data suggest a model in
which HoxBC functions as a hydrogen receptor which interacts either
directly or indirectly with the sensor kinase HoxJ. Furthermore, unlike
in most other two-component regulatory systems, the
autophosphorylation-active kinase acts negatively on hydrogenase gene
expression. This observation indicates that the HoxJ-mediated
phosphorylation of the response regulator HoxA blocks hydrogenase gene
transcription. The negative effect of HoxJ is released by HoxBC,
provided H2 is present (25). Proteins similar to
HoxBC, designated HupUV, have been identified in Rhodobacter capsulatus and Bradyrhizobium japonicum. Mutant
analysis revealed that these proteins play a pivotal role in the
H2-dependent regulation in these organisms. These results
led to the conclusion that the HupUV proteins act as a hydrogen sensor
(6, 15).
To study the mechanism of H2-signal transduction in more depth, the interacting partners of the system have to be isolated and characterized in vitro. Because previous attempts to overproduce active [NiFe] hydrogenases heterologously in Escherichia coli had not been successful, we constructed a novel expression vector for the native host R. eutropha. With the aid of this vector, we achieved an efficient expression of hoxBC and show that the resulting protein catalyzes H2 oxidation. The inspection of mutants revealed that the physiological role of HoxBC is H2 sensing and not the generation of energy for growth on H2. Thus, the third hydrogenase of R. eutropha is denoted as the "regulatory hydrogenase" (RH). Both the enzymatic activity and the regulatory function of the RH protein are strictly dependent on the availability of nickel in the medium, showing that nickel is essential for H2 sensing.
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MATERIALS AND METHODS |
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Strains and plasmids.
The strains and plasmids used in this
study are listed in Table 1. Strains with
the initials HF were derived from R. eutropha H16 (wild
type). R. eutropha HF433 harbors an active
H2-sensing signal transduction chain, including the sensor
kinase HoxJ. R. eutropha H16 is a natural variant in which
the H2-dependent signal transduction is interrupted by a
glycine-to-serine exchange at position 422 in HoxJ
(HoxJG422S [25]). The newly isolated
strains R. eutropha HF375, a derivative of strain H16, and
HF459, a derivative of strain HF433, carry in-frame deletions in the
nickel permease gene hoxN. R. eutropha HF500 bears
in-frame deletions in hoxG, hoxH, and
hoxC, resulting in an MBH
SH
RH
phenotype. Strain HF371 (31) harbors the
inactive sensor kinase HoxJG422S in addition to in-frame
deletions in hoxG and hoxH and was used as host
for plasmid-based overexpression of hoxB and
hoxC. E. coli JM109 was used as a host in standard
cloning procedures (53). E. coli S17-1
(43) served as a donor in conjugative transfers.
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allele was subcloned as a 1.5-kb
SalI-fragment into pLO2, yielding pCH659. The fusion sites
in the hoxN
allele and in the PCR amplification products
were verified by sequencing.
Plasmid pCH655, which was used for overexpression of hoxC in
E. coli, was constructed by insertion of a 1.5-kb
PspI (Klenow-treated) fragment harboring the hoxC
sequence without the first two codons into the Ecl136II site
of pQE-30.
Media and growth conditions. Strains of R. eutropha were grown in nutrient broth (NB), in a modified Luria broth (LB) with 0.25% sodium chloride (LSLB), or in mineral salts medium as described previously (12). Synthetic media for heterotrophic growth contained 0.4% (wt/vol) fructose (FN) or 0.2% (wt/vol) fructose and 0.2% (vol/vol) glycerol (FGN). Cultivation under lithoautotrophic conditions was done in mineral salts medium under an atmosphere of hydrogen, carbon dioxide, and oxygen (8:1:1, vol/vol/vol). Sucrose-resistant segregants of sacB-harboring strains were selected on LSLB plates containing 15% (wt/vol) sucrose (27).
E. coli strains were grown in LB medium. Solid medium contained 1.2% (wt/vol) agar. Antibiotics were supplemented with the following: kanamycin (400 µg/ml) and tetracycline (15 µg/ml) for R. eutropha and kanamycin (25 µg/ml), tetracycline, (15 µg/ml), and ampicillin (100 µg/ml) for E. coli.Gene replacement.
The hoxN
allele was
reintroduced into R. eutropha H16 via conjugation using the
suicide vector pCH659. The allelic exchange procedure was based on the
conditionally lethal sacB gene (27). The
resultant sucrose-resistant isolates were screened for the presence of
the desired mutation by amplification of the respective target sites as
previously described (5). Deletion-carrying isolates were
identified on the basis of the altered electrophoretic mobility of the
amplification products. The resulting hoxN
strain HF375
served as the recipient for the hoxJ-containing suicide vector pCH615 to generate the isogenic hoxN
hoxJ strain
HF459. Strain HF500, a derivative of HF371 (31), was
isolated by the same recombination technique using pCH644 which
contains the hoxC
allele (25).
Cell fractionation. Cells were disrupted in a French pressure cell, and the resulting crude extract was separated into soluble and membrane fractions as described earlier (19). Cytoplasmic and periplasmic fractions were separated by a modified version (4) of the procedure of Probst and Schlegel (36).
Immunogenic techniques.
E. coli JM109 cells harboring
the hoxC expression plasmid pCH655 were grown in LB medium
at 30°C to an optical density at 600 nm (OD600) of 0.8. Expression of His6-HoxC was induced by adding IPTG
(isopropyl-
-D-thiogalactopyranoside) to a final
concentration of 1 mM. Cells were harvested after 3 h of induction
and disrupted by two passages through a French pressure cell. Inclusion
bodies which contained most of the His6-HoxC protein were
treated with 6 M guanidinium-HCl. Subsequently, the
His6-HoxC protein was purified using the
Ni-nitrilotriacetic acid Spin Kit (Qiagen, Inc.) according to the
manufacturer's instructions. Purified His6-HoxC was used as antigen for immunization of rabbits (BioGenes GmbH, Berlin, Germany). Proteins were separated by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), transferred to
Protran BA85 nitrocellulose membranes (Schleicher and Scheull), and
identified immunologically according to a standard protocol
(46). HoxC was detected with anti-HoxC serum, diluted
1:1,000, and an alkaline phosphatase-labeled goat anti-rabbit
immunoglobulin G (Dianova, Hamburg, Germany).
Labeling with 63NiCl2. Labeling of hydrogenases with 63NiCl2 was essentially performed as previously described (5). Cells were grown in FGN medium in the presence of 120 nM of 63NiCl2 (6.38 mCi/ml; Amersham-Buchler). Soluble extracts were prepared and subjected to native PAGE. Gels were run in a continuous buffer system consisting of 90 mM Tris, 80 mM borate, and 2.5 mM EDTA (pH 8.3) at 200 V and 4°C for 2,500 V-h. After electrophoresis the gels were dried under vacuum and subjected to autoradiography using a SI 550 storage PhosphorImager (Molecular Dynamics).
Assays.
Hydrogenase assays were performed with cells grown
heterotrophically in FGN medium. SH (hydrogen-NAD+
oxidoreductase; EC 1.12.1.2) activity was determined by photometric recording of the H2-dependent NAD reduction in the soluble
fraction (39). MBH (hydrogen-acceptor oxidoreductase EC
1.18.99.1) and RH activities were photometrically measured in the
membrane fraction using methylene blue as an electron acceptor
(38). Amperometric H2 uptake measurements using
an H2 electrode and methylene blue as an electron acceptor
were done as previously described (35). For in-gel
chromogenic detection of hydrogenase activity (5), soluble
extracts were resolved on native PAGE gels as described above. The gels
were subsequently incubated in H2-saturated 50 mM potassium
phosphate buffer (pH 5.5) containing 0.09 mM phenazine methosulfate and
0.06 mM nitroblue tetrazolium under an atmosphere of H2 at
30°C. O2 uptake assays were performed with whole cells
using a Clark electrode (Rank Brothers Model 10). O2
consumption was recorded amperometrically in 2.7 ml of H2-saturated potassium phosphate buffer (50 mM, pH 7.0) at
30°C. Then, 200 µl of O2-saturated water was added, and
the reaction was started by the addition of 100 µl of cell suspension
which was previously adjusted to an OD436 of 11. H2-independent O2 consumption was monitored in
N2-saturated potassium phosphate buffer.
-Galactosidase assays were performed as described previously (54), and the activities (in units) were calculated according to the Miller method
(33) except that cell density was measured at 436 nm. The
level of protein in extracts was determined by the method of Lowry et
al. (28).
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RESULTS AND DISCUSSION |
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The RH and homologous H2-sensing proteins form a
subclass of [NiFe] hydrogenases.
The regulatory region of the
megaplasmid-borne hydrogenase gene complex in R. eutropha
has previously been extended by three additional open reading frames
(ORFs), designated hoxB, hoxC, and
hoxJ (25, 26). The ORFs fill a gap between
hoxA, the response regulator gene, and hoxN, the
nickel permease gene. Database searches revealed similarity of the
hoxJ product to histidine protein kinases (26)
and of HoxB and HoxC to [NiFe] hydrogenases, in particular to a small
group of proteins which are present in aerobic H2-oxidizing bacteria (Fig. 2). The closest relatives
are the HoxB and HoxC proteins of Alcaligenes
hydrogenophilus (26) and the HupU and HupV proteins of
R. capsulatus (15) and B. japonicum
(6), with sequence identities ranging from 53 to 79%.
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The RH of R. eutropha is a soluble
H2-oxidizing protein located in the cytoplasm.
The
structural similarity to hydrogenases and its role in
H2-sensing implied the fundamental questions whether the RH
catalyzes H2 oxidation and if so, whether the hydrogenase
activity is necessary for its regulatory function. It was not possible
to discriminate the RH activity in wild-type cells clearly from the
MBH- and SH-derived hydrogenase activities. To exclude assay
interferences the MBH
SH
RH+
strain HF371, which carries in-frame deletions in the large subunit genes of the MBH (hoxG
) and the SH (hoxH
),
was grown under heterotrophic, hydrogenase-derepressing conditions and
then tested for H2-oxidizing activity. Soluble extracts of
this mutant showed a low level of H2 uptake activity (1.5 nmol H2/min/mg of protein) measured amperometrically with
methylene blue as the electron acceptor. However, the activity was
clearly above the background level (<0.5 nmol of H2/min/mg of protein) of extracts derived from strain HF500, which is disrupted in all three hydrogenase proteins. Notably, the MBH
SH
RH+ strain HF371 was not able to grow
autotrophically with H2 as the energy source. These results
indicate that the RH is either formed at an extremely low level and/or
that the protein exhibits only poor hydrogenase activity, a finding
which is in agreement with its regulatory role.
SH
RH+ strain HF371
were separated into the cytoplasmic, periplasmic, and membrane
fractions. In order to detect the RH immunologically a
hexahistidine-tagged variant of the HoxC protein was purified from
E. coli to raise a polyclonal antiserum. Immunoblots
developed with this antiserum gave a faint band corresponding to a
52-kDa protein which was exclusively present in the cytoplasmic
fraction (data not shown). The size of this protein was in good
agreement with the molecular mass of 52.4 kDa predicted for HoxC. A
HoxC signal was absent in extracts of the control strain HF500, which lacks all three hydrogenases, showing that the antiserum is specific for HoxC (data not shown). These immunological data are completely in
line with the prediction for a cytoplasmic location of the RH deduced
from the primary sequence. Since dihydrogen is a freely diffusible
molecule, there is no need for the cell to anchor the H2-sensing protein to the membrane.
Homologous overproduction of the RH protein. To get further insight into the biochemical properties of the H2 sensor, the intracellular level of the protein had to be increased. This was achieved by overexpressing the native hoxB and hoxC genes in R. eutropha under the control of the SH promoter (PSH), which directs transcription of the SH operon (42, 54). The HoxA-controlled, homologous system has the advantage that the Hyp proteins, which are required for metallocenter assembly (11), are potentially available for RH maturation. Moreover, PSH is a well-characterized, relatively strong promoter, and the putative ribosome-binding site of the first gene hoxF of the SH operon is in perfect agreement with the consensus in E. coli (42, 54).
The construction of the expression vector is based on three steps, which are described in detail in Materials and Methods. (i) The native hoxB and hoxC genes were tandemly fused to a modified SH promoter region yielding plasmid pCH594 (Fig. 1). (ii) A fragment containing the PSh-hoxBC fusion was transferred to the broad-host-range vector pEDY309 that replicates stably in R. eutropha. (iii) To enhance transcription from PSH, a copy of the hoxA activator gene, governed by the lac promoter, was inserted into pGE377, resulting in the expression vector pGE378 (Fig. 1). Ongoing research in our laboratory showed that the vector system is also suitable for a general application (3, 8, 10). A moderate expression of the cloned genes in slowly growing cells obviously prevents the occurrence of toxic effects and the formation of inclusion bodies. To estimate the effectiveness of the overexpression system, pGE378 was introduced into strain HF371. The resulting transconjugant was grown under hydrogenase-derepressing conditions, and the cells were fractionated into membrane, cytoplasmic, and periplasmic extracts. Immunological analysis showed that the level of HoxC was enhanced significantly and that the protein was located in the cytoplasm (data not shown). A 40-fold increase in hydrogenase activity (58.6 nmol H2/min/mg of protein) was obtained with HF371(pGE378) in comparison with the control strain HF371(pEDY309) (1.5 nmol of H2/min/mg of protein). Nevertheless, even the enhanced RH activity did not support autotrophic growth of the strain with H2 as the sole energy source, again indicating that the RH is not coupled to an energy-generating electron transport process. This conclusion is consistent with the observation that the O2 uptake rates of the strains HF500 (MBH
SH
RH
, HF371 (MBH
SH
RH+), and HF371(pGE378) (MBH
SH
RH++) remained constant at a basal level (30 nmol of
O2/min/mg of protein) upon addition of H2,
whereas the O2 uptake rate of the MBH- and SH-harboring
wild-type cells increased significantly under these conditions from 30 to 120 nmol of O2/min/mg of protein. The results do not
unambiguously show that the RH has no potential for providing energy
for growth, since the experiment did not exclude the possibility that
the RH is linked to an unknown electron transport component that was
not overexpressed by the vector system used.
The function of the RH is nickel dependent.
The structural
similarity with [NiFe] hydrogenases and the ability to react with
H2 raised the question as to whether the enzymatic and the
regulatory functions of the RH depend on nickel. The RH-overproducing
strain HF371(pGE378) was grown under hydrogenase-derepressing conditions in the presence of various concentrations of
NiCl2. Soluble extracts were prepared, and the proteins
were separated by native PAGE and subjected to a hydrogenase-specific
activity staining assay with phenazine methosulfate as the electron
acceptor. The RH activity strictly correlated with the addition of
nickel to the growth medium (Fig. 3A). In
the presence of 1 µM NiCl2 the dye reaction was very
intense and did not occur with cells cultivated under nickel
starvation. The quantitative RH data obtained from extracts with
methylene blue as the electron acceptor (Fig. 3A) supported the
conclusions drawn from the staining assay. The occurrence of double
bands in native PAGE gels indicates that the RH displays different
conformations. We observed that the ratio of the two bands varied with
respect to the preparation. From gel filtration experiments we obtained
evidence that the slowly migrating band correlates with a tetramer
consisting of two RH moieties and that the rapidly migrating band
correlates with the sole RH dimer (M. Bernhard and B. Friedrich,
unpublished results).
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-galactosidase activity was monitored
representatively with a plasmid-based
(hoxK'-'lacZ)
fusion. The result is illustrated in Fig.
4 and shows a clear correlation between
-galactosidase activity and supplementation of NiCl2 to
the medium. As expected, the expression level was low when
H2 was omitted, even with nickel excess. The conclusion
that nickel is essential for H2 recognition by the RH
protein is confirmed by the behavior of strain HF375, in which the
H2-dependent signal transduction is interrupted due to a
lesion in the sensor kinase (Table 1). This strain displayed high-level
hydrogenase gene expression independently of H2 and hence
independently of nickel (Fig. 4).
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groups and one CO molecule at the iron site
(35). The capability of the sensors to oxidize
H2 does not yet allow the conclusion that H2
binding is intimately connected with a redox reaction. Thus,
elucidation of the underlying mechanism of H2 signal
transduction is a fascinating subject of current research in our laboratory.
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ACKNOWLEDGMENTS |
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O. Lenz and L. Kleihues contributed equally to this work.
We are grateful to Edward Schwartz for providing plasmid pEDY305 and for critical reading of the manuscript.
This work was supported by the Deutsche Forschungsgemeinschaft and by the Fonds der Chemischen Industrie.
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FOOTNOTES |
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* Corresponding author. Mailing address: Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestr. 117, 10115 Berlin, Germany. Phone: 49-30-2093-8100. Fax: 49-30-2093-8102. E-mail: baerbel.friedrich{at}rz.hu-berlin.de.
Present address: Max-Planck-Institut für molekulare Genetik,
14195 Berlin, Germany.
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