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Journal of Bacteriology, August 1998, p. 4219-4226, Vol. 180, No. 16
0021-9193/98/$04.00+0
Copyright © 1998, American Society for Microbiology. All rights reserved.
Phosphate Assimilation in Rhizobium
(Sinorhizobium) meliloti: Identification of a
pit-Like Gene
Sylvie D.
Bardin,
Ralf T.
Voegele, and
Turlough M.
Finan*
Department of Biology, McMaster University,
Hamilton, Ontario, Canada L8S 4K1
Received 10 September 1997/Accepted 1 June 1998
 |
ABSTRACT |
Rhizobium meliloti mutants defective in the
phoCDET-encoded phosphate transport system form root
nodules on alfalfa plants that fail to fix nitrogen
(Fix
). We have previously reported that two classes of
second-site mutations can suppress the Fix
phenotype of
phoCDET mutants to Fix+. Here we show that
one of these suppressor loci (sfx1) contains two
genes, orfA and pit, which appear to form an
operon transcribed in the order orfA-pit. The Pit protein
is homologous to various phosphate transporters, and we present
evidence that three suppressor mutations arose from a single thymidine
deletion in a hepta-thymidine sequence centered 54 nucleotides
upstream of the orfA transcription start site. This
mutation increased the level of orfA-pit transcription. These data, together with previous biochemical evidence, show that the
orfA-pit genes encode a Pi transport system
that is expressed in wild-type cells grown with excess Pi
but repressed in cells under conditions of Pi limitation.
In phoCDET mutant cells, orfA-pit expression is repressed, but this repression is alleviated by the
second-site suppressor mutations. Suppression increases
orfA-pit expression compensating for the deficiencies in
phosphate assimilation and symbiosis of the phoCDET
mutants.
 |
INTRODUCTION |
Because phosphate readily forms
insoluble mineral phosphate complexes with other ions found in soil,
the concentrations of soluble or available phosphate detected in soil
solutions are low and generally range from 0.1 to 10 µM
(3). While many Rhizobium strains are able to
grow at these low phosphate concentrations (6), phosphate
limitation often reduces dinitrogen fixation of
legume-Rhizobium interactions by reducing both nodule number and mass (18, 26, 28). In addition, phosphate limitation may
directly affect discrete steps during the nodule formation and
infection process, such as excretion of Nod factors (22) and/or attachment to roots (17). Additional bacterial
phenotypes of symbiotic importance which change in response to
phosphate limitation include the biosynthesis and/or alteration of
rhizobial cell surface carbohydrates such as exopolysaccharides II
(45) and cyclic
-(1,2)-glucans in Rhizobium
meliloti (5) and lipopolysaccharides in Rhizobium
leguminosarum (32).
Our interest in phosphate metabolism in R. meliloti arose
through our genetic analysis of the ndvF locus which is
located on the pExo megaplasmid. The ndvF mutants form
nodules on alfalfa that contain few bacteria and fail to fix
N2 (Fix
) (8, 10). Two genetically
distinct classes (I and II) of second-site mutations (sfx)
which suppressed the ndvF Fix
phenotype were
identified (25), and an analysis of those mutations together
with a characterization of the ndvF locus has been the subject of several recent reports (1, 2, 37). The
ndvF locus was shown to contain four genes,
phoCDET, that encode an ABC-type high-affinity system
for the uptake of phosphate and possibly phosphonates into the cell
(2, 37). The phoCDET mutants were found to
grow poorly in minimal media containing 2 mM orthophosphate
(Pi) as a sole source of phosphorus (2). Class I
suppressor mutations (sfx1, sfx4, and
sfx5) are tightly linked in transduction, and we previously
reported the localization of the sfx1 locus to an 18-kb
BamHI fragment in the cosmid clone pTH56 (25).
Here we show that sfx1 possesses two genes, orfA and pit, and that the deduced Pit protein is homologous with
phosphate transporters such as the Pit protein of Escherichia
coli.
Analysis of class II suppressor mutations revealed that these mapped to
the phoU and phoB regulatory genes and that
disruption of these genes suppressed the Fix
and
Pi growth phenotype of phoCDET
(ndvF) mutants (1). We showed that while the
phoB gene was required for expression of the
phoCDET genes, phoB appeared to play a
negative role in regulating expression of the orfA-pit
genes. Here we demonstrate that the sfx1 mutation is a
promoter-up mutation which increases expression of the
orfA-pit operon and allows Pi uptake via the
OrfA-Pit system in a phoCDET mutant background. We
conclude that this increased Pi uptake is responsible for
the symbiotic phenotype associated with phoCDET
mutations.
 |
MATERIALS AND METHODS |
Bacterial strains, plasmids, media, and growth conditions.
The strains and plasmids used in this work are listed in Table
1. Transcriptional lacZ
fusions to pit were made by subcloning the 2.1-kb
EcoRI fragments from pTH354 (wild type) and pTH380 (sfx1) which included the recF-orfA intergenic
region into the EcoRI site of the reporter plasmid pMP220
(31) to create plasmids pTH376 and pTH365, respectively.
Transcriptional lacZ fusions to orfA were made by
deleting the region between the SphI site located in the
orfA gene and the SphI site of the pMP220
polylinker of plasmids pTH376 and pTH365 to create plasmids pTH378 and
pTH367, respectively.
Plasmids pTH396 and pTH397 were constructed to delineate the fragment
in which the
sfx1 mutation was located. Since the mutation
was suspected to be in the promoter region, the 920-bp
XhoI/
EcoRI
3 and 540-bp
EcoRV
1/
EcoRI
3 fragments
(
EcoRI
3, for example, represents
the
EcoRI at the third site on the plasmid map; see Fig.
3)
of
pTH191 were subcloned as
XhoI/
HindIII and
EcoRV/
HindIII restriction
sites of pBR322,
respectively. The pBR322 vector was chosen because
it is mobilizable by
pRK600 but cannot replicate in
R. meliloti.
To provide a
selectable marker to identify
R. meliloti recombinants,
the
3.4-kb
HindIII fragment of pGS220 containing the
Km
r gene of Tn
5 (
12) was subcloned
into the
HindIII site of the
two subclones.
The growth media used were Luria-Bertani medium (LB) and LB
supplemented with 2.5 mM MgSO
4 and 2.5 mM CaCl
2
(LBmc) with antibiotic
concentrations as previously described
(
8). The phosphate-free
medium was the MOPS
(morpholinepropanesulfonic acid)-buffered
minimal medium described by
Bardin et al. (
1,
2) except
that this medium was
supplemented with a yeast extract fraction
which stimulates growth of
R. meliloti in defined medium (14 µl/liter)
(
41). For the growth experiments, strains grown for 24 h in
LBmc were centrifuged and resuspended in phosphate-free MOPS
medium
(MOPS P0). Twenty microliters of the cells was used to inoculate
5 ml of MOPS P0 (optical density at 600 nm [OD
600],
~0.05), and
these cultures were grown for 24 h under agitation.
This phosphate
starvation step was necessary since, otherwise,
significant growth
occurred in MOPS P0 medium. The OD
600 of
the cultures was adjusted
to 0.2, and 5-µl aliquots were used to
inoculate 5 ml of MOPS
P0 and 5 ml of MOPS supplemented with 2 mM
P
i (MOPS P2). For the

-galactosidase assays, the
LBmc-grown cells, supplemented with
tetracycline at 2 µg/ml for the
strains containing the pMP220-derived
plasmids, were washed once with
MOPS P0 and resuspended in this
medium. Five-milliliter volumes of MOPS
P0 and MOPS P2 were inoculated
with 20 (OD
600, ~0.05) and
5 (OD
600 ~0.015) µl of cells, respectively,
and the
cells were grown for 38 h before the assay was performed.
DNA manipulation and genetic techniques.
Cloning procedures,
including DNA isolation, restriction digestions, ligation, and
transformation, were performed as described by Sambrook et al.
(29). We cloned the wild-type orfA-pit region as
a 4.8-kb HindIII-SacI fragment from Rm1021
DNA into plasmid pUC118. One such plasmid, pTH354, was identified via
colony hybridization by using a formamide-based hybridization solution
at 42°C (described in reference 8) and a
digoxigenin-labeled 4.8-kb HindIII-SacI fragment from pTH90 as a probe. Annealed probe was detected with anti-digoxigenin antibody conjugated to alkaline phosphatase (AP).
Conjugal mating with MT616 as the helper strain, Tn
5
mutagenesis, and homogenizations (with pPH1JI) were performed as
previously
described (
9,
13,
44).
DNA sequencing and sequence analysis.
DNA sequencing of
overlapping deletions was performed on single-stranded DNA by using the
dideoxy chain termination method as described in the U.S. Biochemicals
protocol for the Sequenase 2.0 enzyme and by using
[
-35S]ATP (NEN DuPont). Single-stranded DNA was
obtained from host strain XL-1 Blue (Stratagene) following infection
with the helper phage M13K07 (36). Both DNA strands were
sequenced by using the
20 (lacZ) primer
(5'-GTAAAACGACGGCCAGT-3') and the IS50 primer (5'-TCACATGGAAGTCAGATCCT-3'). The recF-orfA
intergenic region was amplified via the PCR by using primers 41, 5'-AAGTCGCTCAGTTTCAGGCGTGTGAGA-3', and 55, 5'-CCCATGACGGTGCGCGAATGATCGG-3' (see Fig. 4). Following gel
purification, the sequences of the amplified 359- and 360-bp fragments
were determined on an ABI automated DNA sequencer by using the
above-described primer 41.
AP and
-galactosidase assays.
The AP activity was
measured as described by Yarosh et al. (44) except that the
cells were centrifuged before the OD420 was measured. The
AP activity was calculated by using the following formula: (1,000 × OD420)/(OD600 ×
T), with
T being the reaction time (in minutes).
The

-galactosidase assay was performed, and specific activities in
Miller units were calculated as previously described (
1).
Determination of transcriptional start sites.
Total RNA was
isolated from MOPS P2 medium-grown cells by using the procedure
outlined in the RNeasy Midiprep kit (Qiagen). Three different primers
(primers 55, 81, and 82 [see Fig. 4]) were labeled with
[
-33P]ATP (NEN Dupont) and polynucleotide kinase
(NEB). Thirty micrograms of RNA was annealed to labeled primer (4 × 105 to 1.5 × 106 cpm) and extended
with Moloney murine leukemia virus reverse transcriptase for 90 min at
42°C. To align the transcriptional start sites, the same primers were
used in conjunction with template DNA (pTH191, sfx1) in a
standard sequencing reaction by using the Sequenase kit (Amersham,
Oakville, Ontario, Canada).
Transport assays.
For transport assays, cells were
precultured in LBmc, washed three times with MOPS P0, and subcultured
into MOPS P2. Cells grown aerobically for 24 h at 30°C were
harvested by centrifugation, washed four times with MOPS P0, and
resuspended to an OD600 of 10 in MOPS P0. Cells were
diluted 1:20 into MOPS P0 and equilibrated for 5 min at 30°C. Uptake
was initiated by the addition of [33P]orthophosphoric
acid (NEN DuPont) to a final concentration of 4 µM (175 Ci/mol).
Aliquots were removed from the assay at different time points, placed
on Millipore HAWP 02500 nitrocellulose filters (0.45-µm pore size;
presoaked in 1 M
K2HPO4-KH2PO4 [pH
7.0]), and immediately washed with 40 mM MOPS-20 mM KOH-20 mM
NH4Cl-100 mM NaCl-1.2 mM CaCl2-2 mM
MgSO4. Filters were dried, placed in scintillation liquid
(BCS; Amersham), and counted. All transport assays were performed in
triplicate.
 |
RESULTS |
sfx1 suppresses the Pi transport and growth
phenotypes of phoCDET mutants.
Subsequent to
the identification of sfx1 as a second-site mutation which
suppressed the Fix
symbiotic phenotype of
ndvF mutants (25), we established that the
ndvF locus contains four genes, phoCDET,
which encode a phosphate transport system (2). Since
phoCDET mutants grow slowly in medium containing 2 mM
Pi and are defective in Pi transport
(2), we wished to determine whether sfx1
restored a wild-type growth and phosphate transport phenotype to
phoCDET mutants.
Results from growth experiments showed that while the
R. meliloti phoC
490 mutant, RmG490, grew
slowly relative to the wild
type, Rm1021, in medium containing 2 mM P
i, the doubling time
for the
phoC
490
sfx1 strain, RmG762, was similar to that of the
wild
type (Fig.
1). Additional
experiments revealed that
sfx1 also suppressed the
slow-growth phenotype observed when either
the
phoCDET
deletion (

G439) mutants or the
phoT
491 insertion
mutants were grown in MOPS-2 mM P
i (data not shown).

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FIG. 1.
Growth of Rm1021 (wild type) ( ), RmG490
(phoC 490) ( ), RmG762 (phoC 490
sfx1) ( ), RmG822 (phoC 490 sfx1
orfA23::Tn5) ( ), RmG830
(phoC 490 sfx1 pit10::Tn5)
( ), and RmH842 (phoC 490 sfx1
recF12::TnphoA) ( ) in MOPS-buffered minimal
medium supplemented with 2 mM Pi. Each time point represent
the average of triplicate values. The growth curve for strain RmG821
[phoC 490 sfx1
(orf2)2::Tn5] was similar to that
for strain Rm1021, and the growth curves for phoC 490
sfx1::Tn5 recombinants 16, -3, -J, -5, and
-10A (Fig. 3) were similar to those for RmG822 and RmG830. In order to
simplify the figure, these results are not shown.
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|
Measurements of the transport of
33P-labeled
inorganic phosphate into cells revealed that the rate of
P
i uptake in the
phoC mutant RmG439 was
reduced relative to that of the wild type, Rm1021,
whereas uptake
into the
phoC sfx1 mutant strain, RmG762, was restored
to the wild-type level (Fig.
2).
Moreover, strain RmG830, which
carries the
phoC
490 mutation together with a Tn
5
insertion in
the
sfx1 locus
(
pit10::Tn
5), showed P
i uptake
rates similar to
those of the
phoC mutant RmG490. These
results established that
the
sfx1 mutation restored
wild-type phosphate transport and growth
phenotypes to the
phoC mutant. To further investigate the genetic
nature
of the
sfx1 locus, we first delineated the minimal gene
region required for
sfx1-mediated suppression.

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FIG. 2.
Pi uptake in different R. meliloti mutants. [33P]orthophosphoric acid
was added to a final concentration of 4 µM. Results for
R. meliloti Rm1021 (wild type) ( ), RmG490
(phoC 490) ( ), RmG762 (phoC 490
sfx1) ( ), and RmG830 (phoC 490
pit10::Tn5) ( ) are shown. The symbols
represent the means of triplicate assays, and each line gives the
linear regression for all data points for one strain. Background values
for all strains were adjusted so that the results for the extrapolated
zero time showed no Pi uptake.
|
|
Localization and nucleotide sequence of sfx1.
The
sfx1 locus was previously located to the 18-kb
BamHI fragment on the pTH56 cosmid (25), and as a
first step in the delineation of sfx1, a 12-kb
HindIII fragment internal to the 18-kb region was
subcloned into pRK7813 to give pTH90. This fragment contained the
entire sfx1 locus since RmG490 (phoC
490)
pTH90 transconjugants formed Fix+ nodules on alfalfa and
grew like the wild-type strain in medium containing 2 mM phosphate
(data not shown). Tn5 insertions which mapped within the
12-kb insert of pTH90 were isolated, and seven of these plasmids
were used to generate pTH90 deletion derivatives in which various
amounts of the 12-kb insert region had been removed (Fig.
3, upper diagram). Fragments from the
12-kb region were also subcloned into pRK7813 (Fig. 3). The symbiotic
Fix phenotype and/or phosphate growth phenotype of RmG490
(phoC
490) transconjugants carrying the various
plasmids allowed us to deduce that the entire sfx1 locus was
located between the EcoRI1 and
EcoRV1 sites indicated on the map of pTH276 in
Fig. 3.

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FIG. 3.
Restriction maps of pTH90 and related plasmids. The
upper diagram shows the regions which remained following deletion from
the BamHI site within Tn5 transposons ( 2.15,
-1.4, -1.5, -E, -2.3, -3.10, and -2.2) to the BamHI site in
the polylinker of pTH90. Below the map for pTH276 are diagrammed the
deduced orfA-pit genes and two partial recF and
orf2 open reading frames together with the Tn5
insertions that disrupted the sfx1 locus ( 16, -3, -J, -5, -10, -23, and -10A) and the 2 and 12 insertions that did not. The
orientation of fragments subcloned into pRK7813 are indicated relative
to the position of the plac promoter. The subclones are
pTH276 (4.8-kb HindIII/SacI), pTH305 (2.6-kb
HindIII/EcoRV1), pTH304 (2.5-kb
HindIII/SmaI1), and pTH347 and
pTH348 (2.6-kb partial EcoRI in orientations I and II). The
ability of the plasmids to suppress the Fix and/or
slow-growth phenotype of RmG490 (phoC 490) in MOPS P2
is indicated in parentheses (+, suppression; , no suppression).
Restriction site abbreviations: B, BamHI; Bg,
BglII; C, ClaI; H, HindIII; R,
EcoRI; Sc, SacI; Sm, SmaI; Sp,
SphI; V, EcoRV; X, XhoI. The
subscripts following the R and V are used to specify particular
sites.
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|
Transposon insertions within this region were recombined into the
RmG762 (
phoC
490
sfx1) chromosome (Fig.
3),
and the physical
structure of the resulting recombinants was confirmed
by Southern
blot analysis (data not shown). The

2 and

12
recombinants grew
like the suppressor strain RmG762 in MOPS medium
containing 2
mM P
i, whereas the

16, -3, -J, -5, -10, -23, and -10A recombinants
grew poorly (data not shown and Fig.
1). In addition,

10 and

23 recombinants formed
Fix

nodules when tested on alfalfa plants (data not
shown). These
results confirmed that
sfx1 was located
between the

2::Tn
5 insertion
and the
EcoRI
3 site. The nucleotide sequence of
this 2,828-bp
region was determined.
Analysis of the nucleotide sequence of the sfx1
locus.
Analysis of the nucleotide sequence revealed the presence
of two complete open reading frames designated orfA and
pit (see below) and (Fig. 3). The orfA stop codon
(TGA) and the pit start codon (ATG) overlapped at the
adenosine, suggesting that both genes are transcribed as a single
transcript. The G+C contents of orfA and pit were
62 and 64%, respectively. There was a strong bias for G and C at the
third position of the codons (83% for orfA and 87% for
pit). This bias together with the codon usage of
orfA and pit suggested that these genes were
expressed in R. meliloti (24, 38).
A partial open reading frame initiating 234 bp upstream from
orfA and whose 176-amino-acid product is homologous to the
N-terminal
regions of many RecF proteins, including
Caulobacter
crescentus (
27), was detected (Fig.
3). An additional
partial open reading
frame (designated
orf2), initiating 114 bp downstream of
pit,
was also found. Neither
recF nor
orf2 was part of the
sfx1
locus
since
recF
12::Tn
5 and
orf2
2::Tn
5 recombinants of strain RmG762
(
phoC
490
sfx1) retained the suppressor
phenotype (see above).
An ATG start codon preceded by a potential
ribosome binding site
was found for each gene (CGGA-N6-ATG for
recF, TGGA-N6-ATG for
orfA, GAGA-N7-ATG for
pit, and GAGA-N7-ATG for
orf2).
GenBank searches (
16) revealed that the 334-amino-acid
R. meliloti Pit protein (RmPit) was similar in sequence
to a large
family of prokaryotic and eukaryotic phosphate transport
proteins
(
42,
43; for a review, see reference
20), including the
low-affinity Pit phosphate
transport protein of
E. coli (accession
no.
P37308; EcPitA)
(
30) and the phosphate-repressible phosphate
permease
of
Neurospora crassa (accession no.
P15710;
NcPho-4
+) (
21). In addition, RmPit showed
similarity to numerous uncharacterized
proteins, including the HI1604
protein of
Haemophilus influenza (accession no.
P45268)
(
15) and the EcPitB protein of
E. coli (accession
no.
P43676) (
4). Consistent with its homology
to
P
i transport proteins, an analysis of the RmPit sequence
employing
the TopPred II program (
11) revealed nine
"certain" membrane-spanning
domains.
GenBank searches revealed that the 214-amino-acid OrfA protein had 21%
amino acid identity with the deduced 226-amino-acid
HI1603
protein of
H. influenzae (accession no.
P44271)
(
15).
This result was interesting since the
HI1603 gene is located directly
upstream (25 bp) from the
pit-like
HI1604 gene of
H. influenzae (see above). The conserved location of
orfA-pit-like genes
suggests
that they are functionally related.
The sfx1 mutation contains a single T deletion in a
hepta-T sequence upstream of orfA.
To investigate whether
the sfx1 mutation lay in the orfA-recF intergenic
region, the XhoI/EcoRI3 and
EcoRV1/EcoRI3 fragments from the sfx1 locus (Fig. 3) in plasmids pTH396 and
pTH397, respectively, were recombined via a
Campbell-type single crossover into the RmG490
(phoC
490) genome (see Materials and Methods).
The presence of the sfx1 mutation was then determined by
screening the recombinants for suppression of the mucoid colony
phenotype of phoCDET mutants as observed on
low-osmolarity GYM medium (25). Of 70 pTH396 recombinants examined, 12 formed dry colonies and thus suppressed the mucoid phenotype of RmG490. On the other hand, of 70 pTH397 recombinants examined, none showed a suppressor phenotype.
Together, these data indicated that the sfx1 mutation lay in
the orfA-recF intergenic region.
The nucleotide sequence of the
XhoI/
EcoRV
1 fragments from the
sfx1 locus in pTH380 and the wild-type locus in pTH354 were
determined. Both sequences were identical, except that a run of
seven
thymidines, present in the wild-type sequence at positions

80 to

86
upstream from
orfA, was reduced to six thymidines in
the
sfx1 mutant sequence (Fig.
4).
A 359-bp fragment containing
the complete
recF-orfA
intergenic region was PCR amplified from
the wild type, Rm1021, and the
two other class I suppressor strains,
RmG203 (
sfx4) and
RmG204 (
sfx5) (
25). The nucleotide sequences
of
the amplified fragments revealed that all three were identical
except
that
sfx4 and
sfx5 mutant sequences, like the
sfx1 sequence,
contained six thymidine residues in place of
the seven thymidines
present in the wild-type sequence. Thus, all three
independently
isolated class I suppressor mutants (
sfx1,
sfx4, and
sfx5) carried
the same thymidine
deletion mutation. While this finding was surprising,
we note that
repeat sequences, such as the run of seven thymidines,
are known to be
mutational hot spots (
23).

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FIG. 4.
Determination of the orfA transcriptional
start sites. The autoradiograph shows the products of the sequencing
reaction by using primer 55 and plasmid pTH191 (sfx1) as a
template. The results for primers 81 and 82 yielded a start site
identical to that with primer 55 (data not shown). The relevant
sequence is shown on the left, and the arrow indicates the position of
the extension product. Lane 1, RmG591 (sfx1) carrying pTH347
(sfx1 orfA-pit in orientation I); lane 2, RmG591; lane 3, Rm1021 (wild type); lane 4, Rm1021 carrying pTH391
(orfA-pit); lane 5, RmG591 carrying pTH348 (sfx1
orfA-pit in orientation II). The sequence on the right of the
figure is the wild-type recF-orfA intergenic region. The
deduced orfA transcriptional start site is in boldface type
and underlined. The translational start sites for orfA and
recF are in boldface type with arrows above indicating the
direction of transcription. The three different primers used are
indicated by thin underlines. The hepta-thymidine repeat is underlined,
and a consensus PHO box sequence is shown below the putative
PhoB-binding site. Numbers to the right of the sequence are nucleotide
positions relative to the orfA transcriptional start site.
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sfx1 increases orfA and pit
expression.
To investigate whether the sfx1
mutation altered the level of orfA-pit expression, we
constructed transcriptional lacZ fusions to the
orfA and pit genes from both the wild-type and
sfx1 loci in the broad-host-range reporter plasmid pMP220
(see Materials and Methods). The resulting plasmids were transferred
into the wild-type Lac
R. meliloti
strain, RmG212, and the
-galactosidase (Fig.
5b) and AP (Fig. 5a) activities of the
transconjugants were measured after 38 h of growth in
MOPS-buffered medium containing either no phosphate (MOPS P0) or 2 mM
inorganic phosphate (MOPS P2). High and low AP activities confirmed
that the cells were grown under phosphate-deficient and
phosphate-sufficient conditions, respectively (Fig. 5a, data sets 1, 2, and 4).

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FIG. 5.
Histogram showing AP (a) and -galactosidase (b)
activities from the R. meliloti wild type (wt), RmG212,
and the RmG212 phoC mutant, RmH667. The strains
represented in data sets 2 to 5 carried plasmid-borne lacZ
gene fusions to the pit or orfA genes from the
wild-type and sfx1 loci, i.e., plasmids pTH376, pTH378,
pTH365, and pTH367, respectively. Cells were assayed following 38 h of growth in MOPS-buffered minimal medium with no phosphate added
( ) or supplemented with 2 mM phosphate ( ). Each datum point
represents the average of triplicate values ± standard error
(error bar).
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The results revealed, first, that both
pit and
orfA expression levels from the
sfx1 locus were
three and five times higher,
respectively, than expression from the
wild-type locus (Fig.
5b,
data sets 2 and 4). Second,
orfA
and
pit expression was higher
in cells cultured with excess
P
i (MOPS P2) than in cells cultured
with phosphate
limitation (MOPS P0). Third, the level of
orfA expression
was three- to fivefold higher than the level of
pit expression. In summary, the
sfx1 mutation increased the
level
of
orfA-pit expression and both
sfx1- and
wild-type-directed expression
appeared to be controlled via the
phosphate concentration in the
medium.
Since the
sfx1 mutation exerts its phenotypic effect
in a
phoCDET (
ndvF) mutant background,
we also measured both
orfA and
pit
expression in a
phoC Lac

background
(RmH667). In this background, levels of both
orfA and
pit expression directed from the wild-type locus were very
low regardless of whether the cells were cultured in the presence
(2 mM) or absence of inorganic phosphate (Fig.
5b, data sets 3
and 5). On
the other hand, while the expression of
sfx1-orfA and
sfx1-pit gene fusions was reduced by 23 to 30% in the
phoC mutant
relative to that in a wild-type background,
their levels of expression
were still two to three times higher than
the levels of the corresponding
wild-type fusions in a wild-type
background. A two- to threefold
increase in
orfA-pit
expression thus appears to be sufficient
to allow suppression of the
phoCDET phenotypes. We note that the
high AP activity
detected in
phoC mutant cells cultured in medium
containing 0 or 2 mM P
i suggests that these cells are
starved
for P
i (Fig.
5a, data sets 3 and 5) (see also
reference
1).
The modest increase in
orfA-pit transcription which resulted
from the
sfx1 mutation prompted us to determine whether an
increase
in the copy number of the wild-type
orfA-pit locus
would be sufficient
to allow the
phoC mutant to grow in
medium containing 2 mM P
i.
The wild-type and
sfx1
orfA-pit gene regions were therefore cloned
into the
broad-host-range vector pRK7813, and RmG490 (
phoC)
transconjugants
carrying these plasmids (pTH391 and pTH348,
respectively) grew
like the wild-type strain, Rm1021, in MOPS P2
(data not shown).
We therefore conclude that the increase in
orfA-pit expression
resulting from the increase in the copy
number of the wild-type
locus is sufficient to suppress the slow growth
of the
phoC mutant
in medium containing 2 mM
P
i.
The orfA-pit transcriptional start site lies 29 bp
upstream of orfA.
To investigate the relationship between
the sfx1 mutation and the orfA-pit promoter, we
mapped the orfA transcriptional start site by primer
extension analysis. mRNA was isolated from strains in which the copy
numbers of the sfx1 and wild-type orfA-pit
regions were increased via the plasmids pTH391 and pTH348,
respectively. A single transcriptional start site, lying 29 bp upstream
from orfA, was identified with three separate primers (Fig.
4 and data not shown). The extension product observed from cells
carrying additional copies of the wild-type orfA-pit gene
region was much less intense than the product from cells carrying
additional copies of the sfx1 locus (Fig. 4, lanes 1, 4, and
5). Moreover, in strains carrying only the chromosomal copy of the
orfA-pit gene region, a faint extension product was observed
with mRNA isolated from sfx1 strains while no product was
detected in wild-type cells (Fig. 4, lanes 2 and 3). These results
confirmed that the sfx1 mutation increased orfA
transcription, and the data also suggest that under growth
conditions (2 mM Pi) in which the wild-type orfA-pit operon is maximally expressed, the actual level
of transcription is low. These conclusions are consistent with the
results from lacZ gene fusion studies described above.
We identified

10 and

35 consensus-like hexamers (TAT GAC
and TTTCCC, respectively), followed by the
hepta-thymidine repeat
(

51 to

57), upstream from the
transcriptional start site. Partially
overlapping the
heptathymidine repeat site of the
sfx1 mutation,
we
identified an 18-bp element which contained 11 bp identical
to the
consensus binding site for the
E. coli PhoB protein
(Fig.
4).
 |
DISCUSSION |
The data presented in this report and previous biochemical data
(37) suggest that the orfA-pit operon of
R. meliloti encodes a phosphate transport system whose
expression is regulated by the amount of available inorganic
phosphate. The orfA-pit genes are expressed in cells
grown in the presence of excess phosphate (2 mM Pi),
whereas under Pi limiting conditions orfA-pit
transcription is repressed (Fig. 5). Unlike the latter wild-type
pattern of orfA-pit regulation, our data show that in
phoCDET mutant cells, transcription of the
orfA-pit operon is repressed, even in cells cultured with
excess Pi (2 mM) (Fig. 5b, data sets 3 and 5). Thus, phoCDET mutants grow poorly in medium containing 2 mM
Pi and show a reduced Pi transport phenotype
not because they lack the PhoCDET transport system but because
orfA-pit expression is repressed. Hence, the Pi
assimilation phenotypes resulting from phoCDET mutations are eliminated by secondary mutations such as sfx1 which
increase orfA-pit transcription. The fact that
sfx1 was identified as a suppressor of the Fix
phenotype of phoCDET mutants reinforces the suggestion
that the phoCDET Fix
phenotype is a direct
consequence of the Pi assimilation phenotype of these
mutants.
In E. coli and Acinetobacter johnsonii, there is
physiological evidence that a Pit-like phosphate transport
system, which transports Pi as a neutral metal
phosphate complex, operates during conditions of Pi excess
and that under Pi limiting conditions a separate
high-affinity phosphate transport system is employed for Pi
uptake (PstSCAB in E. coli) (33-35, 39, 40).
While the proposed role for the Pit protein in R. meliloti is similar to that of the E. coli Pit protein,
our data clearly suggest that orfA-pit expression is
phosphate regulated in R. meliloti whereas the E. coli Pit transport system is believed to be constitutively expressed (40).
Why phoCDET mutations result in repression of
orfA-pit expression is unclear. However, we recently showed
that this repression is mediated through the transcriptional activator
PhoB since mutations which inactivate the phoB gene relieve
this repression (1). In wild-type cells, PhoB also appears
to mediate the phosphate-dependent regulation of orfA-pit
expression, since orfA-pit expression is constitutive in a
phoB mutant background (1). In view of the above
data, it is particularly interesting to find a PhoB-like binding site
in the orfA promoter. In E. coli, genes whose
expression is activated by PhoB contain a PhoB binding site in the
35
region of the promoter. Similarly, the R. meliloti
phoC promoter contains a PhoB-like binding site in the
35
region, and phoC expression is positively regulated by
phoB (2). The PhoB-like binding site of the
R. meliloti orfA-pit wild-type promoter is centered at
62.5, and we suggest that this atypical positioning reflects the
negative regulation of orfA-pit expression by PhoB.
While the single thymidine deletion (sfx1) mutation
increases the basal expression and strength of the
orfA-pit promoter, expression is still regulated by the
level of available phosphate. Indeed, the sfx1 mutation
appears to increase the sensitivity of the orfA-pit promoter
to regulation by phosphate, since sfx1-directed orfA-pit transcription was Pi regulated in both
the wild-type and phoC backgrounds (Fig. 5b, data sets 2 to 5), whereas (as noted above) wild-type orfA-pit showed
only very low expression in the phoC background (Fig.
5b, data sets 3 and 5). Given the location of the sfx1
mutation and PhoB-like binding site (Fig. 4), it is not surprising
that sfx1 transcription is still subject to
phosphate-dependent regulation. Further studies are clearly required to
verify the PhoB binding site and to investigate how the deletion
mutation increases the strength of the orfA-pit promoter.
 |
ACKNOWLEDGMENTS |
This work was supported by operating and strategic grants from
the Natural Sciences and Engineering Research Council of Canada to
T.M.F.
We thank Nathan Falcioni for technical assistance in identifying the
sfx3 and sfx4 mutations, Bob Watson for the yeast
extract fraction, and all members of the Finan laboratory for comments and discussions.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Biology, McMaster University, 1280 Main St. West, Hamilton, Ontario, Canada L8S 4K1. Phone: (905) 525-9140, ext. 22932. Fax: (905) 522-6066. E-mail: FINAN{at}MCMASTER.CA.
 |
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