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Applied and Environmental Microbiology, March 2000, p. 937-942, Vol. 66, No. 3
Laboratorio de Microbiología, Escuela
Técnica Superior de Ingenieros Agrónomos, Universidad
Politécnica de Madrid,1 and
Consejo Superior de Investigaciones
Científicas,2 Ciudad Universitaria
s/n, 28040 Madrid, Spain
Received 5 August 1999/Accepted 29 November 1999
A limited number of Rhizobium and
Bradyrhizobium strains possess a hydrogen uptake (Hup)
system that recycles the hydrogen released from the nitrogen fixation
process in legume nodules. To extend this ability to rhizobia that
nodulate agronomically important crops, we investigated factors that
affect the expression of a cosmid-borne Hup system from Rhizobium
leguminosarum bv. viciae UPM791 in R. leguminosarum
bv. viciae, Rhizobium etli, Mesorhizobium loti,
and Sinorhizobium meliloti Hup Hydrogen production due to
nitrogenase activity is a source of inefficiency in
Rhizobium-legume symbioses. Certain rhizobial strains
synthesize a hydrogen uptake (Hup) system that recycles the hydrogen
that evolves during the N2 fixation process. This ability
to utilize H2 reduces energy losses and has been shown to
enhance legume productivity (11, 12).
In symbiosis with peas, Rhizobium leguminosarum bv. viciae
UPM791 induces a [NiFe] hydrogenase whose genetic determinants have
been isolated in cosmid pAL618 (24). A sequence analysis of
the 20-kb DNA region cloned in this cosmid revealed the presence of a
gene cluster (hupSLCDEFGHIJK hypABFCDEX) required for the Hup+ phenotype (19, 25, 33, 34, 36). The
hupSL genes code for the hydrogenase structural polypeptides
which exhibit high levels of sequence similarity with hydrogenase
structural subunits from other bacteria (for reviews see references
14 and 46). The remaining
hup and hyp genes are necessary for synthesis of an active hydrogenase, although the specific functions of most of these
genes have not been determined yet. Unlike the Bradyrhizobium japonicum system, the R. leguminosarum Hup system is
induced only during symbiosis through regulators involved in the
nitrogen fixation process (41). Expression of the
hupSL genes is observed only in pea bacteroids and has been
shown to be controlled by the nitrogenase regulatory protein NifA
(4). In contrast, hyp genes are induced under
microaerobic conditions as well as under symbiotic conditions by the
transcriptional activator FnrN (17, 18). The R. leguminosarum UPM791 hydrogenase is posttranslationally activated
by a nickel-dependent processing system that requires hup
and hyp gene products (6). During this process,
the immature small (HupS) and large (HupL) structural polypeptides are
converted into active forms in the presence of nickel. Processing of
the large subunit has been studied in detail with Escherichia
coli hydrogenase 3. In this system, which is highly homologous to
the R. leguminosarum system, the precursor HycE large
subunit is converted into its mature form by removal of a C-terminal
32-amino-acid peptide (38). This proteolytic processing step
is carried out by a specific protease encoded by the hycI
gene (39), which is homologous to the hupD gene
of R. leguminosarum, and depends on the presence of nickel. Consistent with this requirement, adding nickel to an R. leguminosarum UPM791-pea symbiosis system results in a significant
increase in hydrogenase activity, indicating that the availability of
nickel to plants can be a limiting factor for hydrogenase activity in symbioses (6).
The ability to utilize H2 is a desirable characteristic for
generating more productive and efficient rhizobial inoculants (12,
28). Unfortunately, this phenotype has been found only in a few
Rhizobium and Bradyrhizobium strains
(10). Thus, extension of this ability to other rhizobia has
obvious biotechnological interest and has been the aim of several
previous studies (1, 23, 29, 45). In our laboratory we have
tried to generate genetically engineered Rhizobium strains
with high energy efficiency by introducing the hydrogen oxidation
system from R. leguminosarum bv. viciae UPM791. In order to
incorporate the ability to recycle H2 into rhizobia that
nodulate agronomically important crops, we studied factors that affect
expression of the hydrogenase system in different rhizobial
backgrounds. In this study we analyzed the expression of cosmid-borne
hup genes from R. leguminosarum bv. viciae UPM791
in R. leguminosarum bv. viciae, Rhizobium etli, Mesorhizobium loti, and Sinorhizobium meliloti
Hup Bacterial strains, plasmids, and growth conditions.
The
rhizobial strains used in this study were R. leguminosarum
bv. viciae UPM791 (26), UML2 (25, 40), and PRE
(5, 27), R. etli CFN42 (25, 32),
S. meliloti 102F34 (8), and M. loti Y3
and U226 (29). Cosmid pAL618 is a pLAFR1 (Tcr)
derivative harboring the hydrogenase gene cluster from R. leguminosarum bv. viciae UPM791 (24). Cosmids pHL55,
pHL14, and pHL12 are pAL618 derivatives carrying lacZ
fusions due to insertion of a Tn3HoHo1 transposon
(31) (Fig. 1). These cosmids
were introduced into Rhizobium strains by triparental mating
by using pRK2073 as a helper plasmid and the procedure of Ditta et al.
(9). Transconjugants were selected on Rhizobium
minimal medium (30) supplemented with tetracycline (5 µg · ml
0099-2240/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Nickel Availability and hupSL Activation by
Heterologous Regulators Limit Symbiotic Expression of the
Rhizobium leguminosarum bv. Viciae Hydrogenase System in
Hup
Rhizobia

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ABSTRACT
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
strains. After
cosmid pAL618 carrying the entire hup system of strain
UPM791 was introduced, all recipient strains acquired the ability to
oxidize H2 in symbioses with their hosts, although the
levels of hydrogenase activity were found to be strain and species
dependent. The levels of hydrogenase activity were correlated with the
levels of nickel-dependent processing of the hydrogenase structural
polypeptides and with transcription of structural genes. Expression of
the NifA-dependent hupSL promoter varied depending on the
genetic background, while the hyp operon, which is
controlled by the FnrN transcriptional regulator, was expressed at
similar levels in all recipient strains. With the exception of the
R. etli-bean symbiosis, the availability of nickel to
bacteroids strongly affected hydrogenase processing and activity in the
systems tested. Our results indicate that efficient transcriptional
activation by heterologous regulators and processing of the hydrogenase
as a function of the availability of nickel to the bacteroid are relevant factors that affect hydrogenase expression in heterologous rhizobia.
![]()
INTRODUCTION
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
strains. Our results indicate that both
hup gene transcription by heterologous regulators and the
availability of nickel to plants are critical factors that affect
hydrogenase activity in heterologous hosts.
![]()
MATERIALS AND METHODS
Top
Abstract
Introduction
Materials and Methods
Results
Discussion
References
1). E. coli HB101 used for
matings was grown in Luria-Bertani medium. Rhizobium strains
were grown in TY medium (2) or in yeast mannitol medium
(YMB) (47). To determine cosmid stability in nodules, bacteroid suspensions were serially diluted in YMB and plated onto YMB
agar. One hundred colonies were streaked onto YMB agar with or without
tetracycline, and the frequency of tetracycline-resistant colonies was
calculated.

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FIG. 1.
Physical and genetic map of the hydrogenase gene cluster
from R. leguminosarum bv. viciae UPM791 cloned in cosmid
pAL618. The horizontal arrows below the pAL618 restriction map indicate
the locations and orientations of the hup and hyp
genes. The shaded arrows indicate genes whose encoded products were
detected by an immunoblot analysis in this study. The thin arrows
indicate promoters that control symbiotic expression of hydrogenase
structural genes (P1) (19) or microaerobic
expression of the hypBFCDEX operon (P5)
(18). The vertical lines with black triangles indicate the
sites of insertion and the orientations of the lacZ gene in
pAL618-derived fusion constructs pHL55, pHL14, and pHL12
(31). Restriction sites: E, EcoRI; H,
HindIII; X, XhoI.
Plant tests and enzyme assays.
Pea (Pisum sativum
L. cv. Frisson), bean (Phaseolus vulgaris cv. Negro Jamapa),
alfalfa (Medicago sativa L. ecotype Aragón), and
birdsfoot trefoil (Lotus corniculatus) plants were
inoculated with R. leguminosarum, R. etli,
S. meliloti, and M. loti strains, respectively.
After sterilization in sodium hypochlorite, pea and bean seeds were
pregerminated on 1% agar plates, whereas alfalfa and birdsfoot trefoil
seeds were directly sown. Seeds or seedlings were inoculated with
bacterial cultures and plants were grown under bacteriologically
controlled conditions as previously described by Leyva et al.
(24). The nitrogen-free nutrient solution used was
supplemented with 170 µM Ni2+ chloride salts 10 days
after bacteria were inoculated (6). R. leguminosarum, R. etli, S. meliloti, and
M. loti bacteroids were prepared from nodules of 24-day-old
pea, bean, alfalfa, and birdsfoot trefoil plants, respectively, and
H2 uptake hydrogenase activity was analyzed by the
amperometric method (40). H2 evolution in intact
nodules was determined by chromatography by using a Konik model
KNK-2000 gas chromatograph equipped with a Molecular Sieve 5A column
and a thermal conductivity detector.
-Galactosidase activities in
bacteroid cells were measured as previously described (31).
Immunological detection of Hup and Hyp proteins. HupL and HypB proteins in bacteroid extracts were detected immunologically by using R. leguminosarum HypB-specific antisera (35) and B. japonicum HupL antisera (a gift from R. J. Maier). Immunoblot assays were performed as described by Brito et al. (6). Briefly, crude extracts from bacteroids were resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis on 10% polyacrylamide gels and were transferred onto Immobilon-P membrane filters (Millipore, Bedford, Mass.). The filters were then incubated with a 1:2,000 dilution of the HupL antiserum or a 1:1,500 dilution of the HypB antiserum. Blots were developed by using a secondary goat anti-rabbit immunoglobulin G-alkaline phosphatase conjugate antibody and a chromogenic substrate (bromochloroindolyl phosphate-nitro blue tetrazolium) as recommended by the manufacturer (Bio-Rad Laboratories, Hercules, Calif.).
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RESULTS |
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|
|
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Hydrogenase activity induced by hup genes from R. leguminosarum bv. viciae in heterologous rhizobial
backgrounds.
To identify factors that affect hydrogenase activity
in heterologous backgrounds, hup genetic determinants from
R. leguminosarum bv. viciae UPM791 cloned in cosmid pAL618
(24) (Fig. 1) were introduced into different
Hup
rhizobia. To do this, R. leguminosarum bv.
viciae UML2 and PRE, S. meliloti 102F34, R. etli
CFN42, and M. loti Y3 and U226 were used as recipient
Hup
strains. Transconjugant strains carrying cosmid
pAL618 were used to inoculate the corresponding host plants, which were
grown in a standard nutrient solution, and the ability of bacteroids to utilize H2 was determined (Table
1). The data show that introduction of
cosmid pAL618 resulted in hydrogenase activity in bacteroids of all of
the Hup
strains tested except S. meliloti
102F34. Nevertheless, the activities varied widely among species and
strains. The hydrogen uptake values for bacteroids of R. leguminosarum PRE(pAL618), R. etli CFN42(pAL618), and
M. loti U226(pAL618) were similar to the hydrogen
uptake values obtained for UPM791(pAL618), whereas the levels
of hydrogenase activity of R. leguminosarum UML2(pAL618) and
M. loti Y3(pAL618) bacteroids were lower. In all of these
cases, the activity increased when methylene blue was used as an
artificial acceptor of electrons from hydrogenase. In contrast, very
low levels of hydrogen oxidation when either oxygen or methylene blue
was the electron acceptor were observed in S. meliloti
102F34(pAL618) cultures. High levels of bacteroid hydrogenase activity
resulted in nodules that produced no detectable H2 (strains
derived from R. leguminosarum PRE, R. etli CFN42,
and M. loti U226), whereas R. leguminosarum
UML2(pAL618) and M. loti Y3(pAL618) recycled 80 and 86% of
the H2 evolved by the nitrogenase, respectively. In
contrast, S. meliloti 102F34(pAL618) recycled less than 10%
of the H2 produced in nodules. Cosmid stability was
determined in bacteroid suspensions obtained from plants grown in the
standard nutrient solution (Table 1). The percentages of stability
differed slightly depending on the recipient background. However, the
differences were not correlated with variations in hydrogenase
activity. In particular, similar levels of cosmid maintenance were
observed in strains that exhibited high levels (UPM791 and PRE) and low
levels (UML2 and 102F34).
|
Analysis of Ni-dependent HupL processing. In most of the strains studied, hydrogenase activity increased when nickel was added. This prompted us to study the effect of adding nickel on the HupL status of the bacteroids that had been previously tested to determine their hydrogenase activities. To analyze this effect, we performed Western blot experiments with HupL antibodies raised against the large subunit of the B. japonicum hydrogenase.
Immunodetection of HupL showed that the overall amount of fast-migrating, processed subunits was correlated with the level of hydrogenase activity observed in bacteroids. However, the amount and status of HupL depended on the rhizobial background (Fig. 2A). R. leguminosarum UPM791(pAL618) contained the largest amount of HupL protein, which was detected in two immunoreactive bands at ca. 66 and 65 kDa (Fig. 2A, lanes 1 and 2). A nonspecific band at ca. 50 kDa was also produced. Adding nickel resulted in partial conversion of the slowly migrating inactive band (66 kDa) into the fast-moving active form (65 kDa). This pattern was also observed in bacteroids of R. leguminosarum PRE(pAL618) (Fig. 2A, lanes 5 and 6), indicating that hydrogenase structural proteins are subject to similar levels of synthesis and processing in these two backgrounds. In contrast, a small amount of HupL protein was detected in bacteroids of R. leguminosarum UML2(pAL618) (Fig. 2A, lanes 3 and 4). In this strain, the weak band of processed protein observed under no-nickel-added conditions became slightly stronger when nickel was added. The increase correlated with the increase in hydrogenase activity described above (Table 1). This result indicates that nickel deficiency limits hydrogen uptake in the UML2(pAL618)-pea symbiosis, as was the case with R. leguminosarum bv. viciae strains UPM791 and PRE. However, the small amount of HupL detected in bacteroids of UML2(pAL618) suggests that the level of synthesis of the hydrogenase subunits is the main factor that limits hydrogenase activity in this symbiosis.
|
Analysis of hup and hyp gene
expression.
We studied the observed correlation between the amount
of HupL protein detected and hupL gene expression in certain
strains. To do this, we analyzed transcriptional activation of the
hupL-lacZ fusion borne in cosmid pHL55 (Fig. 1) in R. leguminosarum bv. viciae UPM791, UML2, and PRE, R. etli
CFN42, and S. meliloti 102F34. We also examined
hyp gene expression by using cosmid pHL14, which carries a
hypF-lacZ fusion. As a negative control, we included cosmid pHL12, which harbors a Tn3HoHo1 transposon inserted
in the opposite orientation into the hypD gene (Fig. 1).
Levels of
-galactosidase activity associated with the gene fusions
were measured in bacteroid suspensions of the different transconjugant strains (Table 2). In these bacteroids,
the stabilities of pAL618 derivative fusion constructs were similar to
the stabilities observed for pAL618 (data not shown).
|
-galactosidase activity associated
with the hupL-lacZ fusion (pHL55 construct) revealed that
hup genes were actively transcribed in R. leguminosarum bv. viciae UPM791 and PRE (Table 2). In contrast,
weak induction of the hupL-lacZ fusion was detected in
R. leguminosarum UML2. These results are
consistent with the total amount of HupL protein visualized in the
immunological assays (Fig. 2A). In bacteroids of R. etli
CFN42 and S. meliloti 102F34, the levels of
hupL gene expression were intermediate between the
levels observed in strains UPM791 and UML2 (Table 2), which is also
consistent with the amounts of HupL detected in bacteroids of
CFN42(pAL618) and 102F34(pAL618). These data show that
efficient transcriptional activation of hup genes by
heterologous regulators is a limiting factor for the ability to oxidize
H2 in certain rhizobial backgrounds.
In contrast to hup genes, hyp genes were
efficiently expressed in bacteroids from all symbioses tested, as shown
by the
-galactosidase activity associated with the
hyp-lacZ fusion pHL14 (Table 2). This result is consistent
with the similar levels of HypB protein observed in bacteroids, as
determined by immunoblot experiments (Fig. 2B).
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DISCUSSION |
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In this study we identified factors that affect the
hydrogen-recycling ability induced by cosmid-borne hup genes
from R. leguminosarum bv. viciae UPM791 transferred
into heterologous Hup
Rhizobium strains.
Generation of H2-oxidizing rhizobial strains by
introduction of plasmid-borne hup genes from B. japonicum and R. leguminosarum bv. viciae into other
rhizobia has been described previously (1, 22, 23, 25, 29, 42,
45). In these studies, hydrogenase activities depended on the
bacterial background, as well as on the legume host cultivar. However,
no further efforts were made to explain the observed differences in
hydrogenase activity. This prompted us to study in more detail factors
that affect hydrogenase activity in heterologous hosts. Our data from
immunological assays and our analysis of hup gene expression
highlighted two main factors that affect the efficient expression of
the hydrogenase system in heterologous rhizobial hosts.
The first factor that controls hydrogenase activity is efficient transcription of hydrogenase structural genes in heterologous rhizobia. In contrast to the active expression of hup genes in R. leguminosarum bv. viciae UPM791 and PRE, extremely low levels of hup induction were detected in R. leguminosarum UML2, and only reduced levels were observed in R. etli CFN42 and S. meliloti 102F34. In R. leguminosarum UPM791, hup gene expression is activated by NifA through noncanonical NifA upstream activating sequences (4). Thus, the low level of hup transcription observed in certain backgrounds might be explained by an inefficient recognition of these nonconsensus NifA binding sequences. However, no structural or functional differences in NifA would be expected among strains of the same Rhizobium species, such as R. leguminosarum bv. viciae UML2, UPM791, and PRE (37). Alternatively, differences in hup gene expression could be due to differences in the availability of NifA in the symbioses. There is evidence that the pool of NifA in the cell is strictly regulated in certain rhizobial backgrounds (13). In S. meliloti, overexpression of NifA negatively affects nitrogen fixation (7). In addition, introduction of traits encoded by NifA-regulated genes (nodulation efficiency and transport of dicarboxylic acids) improves symbiosis performance in the presence of additional copies of the nifA gene (3, 43), suggesting that the level of NifA protein can be a limiting factor for gene expression in S. meliloti. Thus, it is reasonable to hypothesize that the levels of NifA available for activation of additional, less canonical promoters could be very low in bacteroids in some symbiotic systems. In contrast, hyp genes are actively transcribed in all of the backgrounds tested. The latter result indicates that the P5 promoter, which is regulated by FnrN in R. leguminosarum bv. viciae (17, 18), is efficiently activated by Fnr type regulators present in different rhizobia, as shown previously for S. meliloti FixK (18, 31).
The second aspect relevant for expression of hydrogenase activity in heterologous backgrounds is the availability of nickel. Previous studies revealed that the nickel content of a plant nutrient solution limits hydrogenase processing and activity in R. leguminosarum bv. viciae pea bacteroids (6). Here, we show that the hydrogenase activities of pAL618-containing bacteroids of R. leguminosarum bv. viciae PRE and UML2, S. meliloti 102F34, and M. loti Y3 and U226 increased when nickel was added. We also demonstrated that hydrogenase activities in Rhizobium-legume symbioses can be correlated with the amount of processed HupL protein detected in bacteroids and that the observed Ni-dependent increases in hydrogen oxidation in these symbiotic systems are a consequence of Ni-dependent HupL processing. Additional evidence suggested that an adequate amount of nickel is required for stability of Hup gene products in some backgrounds, such the M. loti background. In this host, only the processed form of HupL was detected, and the intensity of the immunoreactive band increased when nickel was added. Nickel is not involved in regulation of hup gene expression in R. leguminosarum bv. viciae bacteroids (6). In addition, nickel apparently had no effect on cosmid stability, since the HypB levels were not affected when nickel was added. Consequently, the increase in the amount of the processed HupL protein in M. loti bacteroids from plants grown in the presence of high nickel concentrations was probably due to stabilization of HupL by nickel-dependent processing. On the basis of all of these data we concluded that nickel availability may limit hydrogenase activity in many different Rhizobium-legume symbioses.
It is interesting that the R. etli-Phaseolus system appears to be an exception to the general behavior of Rhizobium-legume systems with regard to the effect of nickel on hydrogenase activity. With this symbiosis, adding nickel to the plant nutrient solution did not alter the level of the processed hydrogenase large subunit and, consequently, did not affect hydrogenase activity. Furthermore, the immature HupL subunit was completely processed at nickel concentrations that limit hydrogenase activity in other symbioses. The availability of nickel to bacteroids depends on the nickel transport capacity of the different rhizobial strains and on the ability of the host plant to provide nickel to the bacteroids. Although the amount of information concerning nickel transport and metabolism in symbiotic bacteria is increasing (15, 16, 44), little is known about this process in plants (20). The lack of information hampers designing strategies which optimize providing nickel to bacteroids. On the other hand, soils with high nickel contents are rare in agricultural systems. For these reasons, a desirable approach for generating Rhizobium inoculants that express the ability to utilize H2 would be to select for symbiotic combinations that exhibit optimized synthesis and processing of the hydrogenase enzyme at low nickel concentrations, as might be the case for the R. etli-bean symbiosis. The immunological test used in this study can be a useful tool for identifying symbiotic partners that exhibit such an optimal ratio.
The analysis described here was aimed at identifying factors that
affect efficient expression of the hydrogenase system in different
Rhizobium hosts in order to extend the ability to oxidize H2 to Hup
rhizobial strains. Our results
suggest that both hup gene expression and the availability
of nickel to bacteroids can be limiting in certain
legume-Rhizobium systems and that adequate attention must be
paid to these factors when new inoculants with high hydrogen-recycling capacity are designed.
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ACKNOWLEDGMENTS |
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We thank R. J. Maier for the generous gift of HupL-specific antisera.
This work was supported by grant PB95-0232 from DGICYT (Spain) and by grant CT960027 (IMPACT 2) from the EU Biotech Programme (both to T.R.-A.), as well as by grant BIO96-0503 from CICYT (Spain) to J.I. B.B. was the recipient of a Contrato de Incorporación de Doctores y Tecnólogos from the Ministerio de Educación y Cultura (Spain).
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FOOTNOTES |
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* Corresponding author. Mailing address: Laboratorio de Microbiología, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain. Phone: 34-91-3365753. Fax: 34-91-3365757. E-mail: jpalacios{at}bit.etsia.upm.es.
Present address: Departamento de Bioquímica, Facultad de
Agronomía, Universidad de la República, CP 11600 Montevideo, Uruguay.
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