Institut für Mikrobiologie,
Eidgenössische Technische Hochschule Zürich, 8092 Zürich, Switzerland,1 and
Institut für Biotechnologie 1, Forschungszentrum
Jülich, 52425 Jülich, Germany2
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INTRODUCTION |
Klebsiella pneumoniae, a
member of the Enterobacteriaceae, is able to grow with
citrate as a sole carbon and energy source under anoxic conditions (for
a review, see reference 4). Citrate fermentation involves
uptake by a Na+-dependent citrate carrier
(32, 44), cleavage into acetate and oxaloacetate by
citrate lyase, and decarboxylation of oxaloacetate to pyruvate by the
Na+ ion pump oxaloacetate decarboxylase
(12, 13). The conversion of pyruvate to acetate, formate,
CO2, and H2 (7,
38) is catalyzed by enzymes generally involved in anaerobic
pyruvate catabolism. The citrate-specific fermentation genes form a
cluster of two divergent operons (5, 6). The
citCDEFG operon encodes citrate lyase ligase (CitC), the
citrate lyase subunits (CitD, CitE, and CitF), and
triphosphoribosyl-dephospho-coenzyme A synthase (CitG), which catalyzes
the formation of a precursor of the citrate lyase prosthetic group
(36, 37). The citS-oadGAB-citAB operon encodes the citrate carrier CitS, the oxaloacetate decarboxylase subunits (OadG, OadA, and OadB), and a two-component system composed of the
sensor kinase CitA and the response regulator CitB (Fig.
1A). The CitA-CitB system was shown to be
essential for the expression of both operons (6). CitA
presumably functions as a sensor of extracellular citrate, since the
periplasmic domain of this membrane-bound protein binds citrate with
high affinity (Kd
6 µM) and
specificity (23). CitB acts as a transcriptional activator of the citS and the citC operons and binds to two
sites in the 193-bp citC-citS intergenic region (Fig. 1) in
a phosphorylation-dependent fashion (24).

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FIG. 1.
Organization of the citrate-specific fermentation genes
in K. pneumoniae. The 13-kb DNA cluster encompassing 11 genes involved in citrate fermentation is shown in panel A. The lower
part shows an enlargement of the
citC-citS intergenic region. The arrows
indicate transcription start sites. The positions of the CitB binding
sites as deduced from DNase I footprints and of putative CRP binding
sites are indicated. The sequence of the
citC-citS intergenic region is shown in
panel B. Indicated are the coding regions, putative ribosome binding
sites (RBS), the transcriptional start sites as determined by primer
extension (25), the 10 regions, the CitB binding sites,
the putative CRP binding sites, and the hypersensitive sites observed
in DNase I footprints (asterisks).
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Maximal expression of a chromosomally integrated translational
citS'-'lacZ fusion requires citrate, anoxic
conditions, and Na+ ions (6).
Whereas the inducing effect of citrate can be attributed to the
CitA-CitB system, the proteins responsible for the regulatory effects
of Na+ and O2 are not yet
known. In citrate minimal media containing glucose or glycerol in
addition, expression of citS'-'lacZ was strongly
reduced (6), supporting previous evidence for
catabolite repression of the citrate fermentation genes (7,
10).
In enterobacteria, the cyclic AMP (cAMP) receptor protein (CRP) is a
key player in catabolite repression (3). A comparison of
the citC-citS intergenic DNA sequence with the palindromic CRP consensus binding site (2) revealed three potential
binding sites for CRP (Fig. 1), one centered at
41.5 bp in front of
the citS transcription start site, another at
41.5 bp in
front of the citC transcription start site, and the third in
between. The
41.5 sites fulfil the exact spacing requirement of class
II CRP-dependent promoters (9, 15), where CRP alone is
sufficient to activate transcription.
In this work we analyzed the effects of glucose, gluconate, and
glycerol on citrate fermentation. Under anaerobic conditions, glucose
is taken up by the phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) and fermented to the products characteristic of butanediol fermentation (1). The
occurrence of this fermentation type in the K. pneumoniae
strain used in this work was confirmed by the detection of the
characteristic product acetoin. Gluconate uptake and fermentation have
not been studied in detail but most likely involve
H+ symport as in Escherichia coli
(20, 31) and the Entner-Doudoroff pathway. Glycerol, which
presumably is taken up a by a glycerol facilitator (46),
is fermented by K. pneumoniae to 1,3-propanediol and acetate
as major products (14, 21, 22). Several of the glycerol
fermentation genes, which form the dha regulon, have been
cloned and sequenced (11, 41-43).
Here we show that glucose, gluconate, and glycerol, despite the
differences in uptake and catabolism, inhibit the expression of the
citrate fermentation genes, thus representing an example of catabolite
repression under fermentative conditions. In addition, evidence for the
involvement of the CRP-cAMP system in this process is provided.
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MATERIALS AND METHODS |
Bacterial strains and culture media
K. pneumoniae ATCC 13882, which is designated the wild
type, was grown as described previously (6). E.
coli DH5
(Bethesda Research Laboratories) was used as a host
for all cloning procedures. E. coli BL21(DE3), which
contains the T7 RNA polymerase gene under the control of the
isopropyl-
-D-thiogalactopyranoside (IPTG)-inducible lacUV5 promoter (39), served as host for
overproduction of the CRP protein from the pET expression plasmid. The
E. coli strains were routinely grown at 37°C either in
Luria-Bertani (LB) medium or in 2× YT medium (34).
K. pneumoniae strain MB1 (6), which contains a chromosomally integrated translational
citS'-'lacZ fusion, was grown in minimal
media containing citrate, glycerol, or both as described previously
(6). For growth experiments, a minimal medium containing
100 mM potassium phosphate buffer (pH 7.0), 50 mM NaCl, 10 mM
(NH4)2SO4, 1 mM
Mg2SO4, and 0.4% trace element solution (180 mM CaCl2, 0.77 mM CoCl2, 0.505 mM
MnCl2, 0.413 mM Na2MoO4, and 7.2 mM
FeSO4) was used. Unless indicated otherwise, potassium
citrate, glucose, potassium gluconate, or glycerol was added as a
carbon source (20 mM). Anaerobic cultures were grown in flasks with
septa at 37°C under nitrogen (150 kPa) without shaking.
Precultures were washed in 100 mM potassium phosphate buffer (pH 7.0)
prior to inoculation. The initial optical density at 600 nm
(OD600) after inoculation was approximately 0.05.
-Galactosidase assays and determination of citrate.
The
-galactosidase assays of strain MB1 grown under various conditions
were performed with permeabilized cells essentially as described by
Miller (25). The citrate content of culture supernatants
was determined spectrophotometrically at 365 nm using a coupled assay
containing 2 U of malate dehydrogenase (pig heart; Boehringer
Mannheim), 1 U of lactate dehydrogenase (hog muscle; Boehringer
Mannheim), and 0.2 to 0.4 U of citrate lyase (Aerobacter aerogenes; Boehringer Mannheim) in a 50 mM glycylglycine buffer at
pH 7.9 in the presence of 2 mM ZnCl2 and 0.5 mM
NADH (5).
Construction of pET-CRP.
Chromosomal DNA of K. pneumoniae ATCC 13882 was used as template for the PCR with Vent
DNA polymerase (New England Biolabs). The primers pCRP-fo
(5'-AGATATACATATGGTGCTTGGCAAACCGCAAAC-3') and
pCRP-re
(5'-GTGGTGCTCGAGTTAACGGGTGCCGTAGACGACG-3')
introduced an NdeI restriction site at the initiation codon
and an XhoI restriction site immediately downstream of the
stop codon (restriction sites are underlined), respectively. The coding
sequence of the primers was designed according to the nucleotide
sequence of the K. aerogenes crp gene (GenBank accession
number M68973). The resulting 655-bp product was cleaved with
NdeI and XhoI and subsequently cloned into pET24b
(Novagen) cut with the same enzymes. The resulting plasmid pET-CRP was
sequenced with T7 promoter and T7 terminator primers. Two positions
were found to differ from that of the published K. aerogenes
sequence: C instead of A at position 12 and A in the place of C at
position 507. These differences, however, do not result in an altered
amino acid sequence.
Purification of CRP and CitBHis.
E.
coli BL21(DE3) containing the expression plasmid pET-CRP was grown
in LB medium including kanamycin (50 µg/ml). The cultures were
incubated at 37°C and 180 rpm until the OD600
reached a value between 0.6 and 0.8. Then, IPTG was added to a final
concentration of 1 mM, and incubation was continued for another
3 h. Cells were harvested by centrifugation, washed once in 20 ml
of buffer A plus 0.2 M NaCl (buffer A consists of 20 mM sodium
phosphate [pH 7.2], 2 mM EDTA, and 5 mM
-mercaptoethanol), and
resuspended in the same buffer (5 g [wet weight]/ml). After addition
of the protease inhibitor diisopropyl fluorophosphate (1 mM) and
0.2 mg of DNase I/ml the cells were disrupted by three passages through a French pressure cell at 108 MPa. Intact cells and cell debris were
removed by centrifugation (30 min at 27,000 × g). The
cell extract was ultracentrifuged (60 min at 150,000 × g), and the resulting supernatant was used for purification
of CRP by affinity chromatography with cAMP agarose (Sigma A0144) as
described previously (47). Purification was monitored by
sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE),
and protein concentrations were determined with the Bradford assay kit
(Bio-Rad Laboratories). Buffer exchange was performed by gel filtration
(PD-10 columns; Pharmacia). CitBHis was
purified by Ni2+ chelate affinity chromatography
as described previously (24).
DNA-protein interaction studies.
For gel retardation assays
of CRP, a 348-bp MluI-SphI DNA fragment covering
the entire intergenic region between citC and citS was labeled with the Klenow fragment of E. coli DNA polymerase I and suitable
-32P-radiolabeled nucleotides according
to the protocol of the manufacturer. Unincorporated nucleotides were
removed using the QIAquick-spin PCR purification kit (Qiagen). An equal
volume of a serial dilution of CRP in TKMD buffer (50 mM Tris-HCl [pH
7.5], 200 mM KCl, 5 mM MgCl2, 5 mM
dithiothreitol) containing 200 µM cAMP was mixed with the DNA
premixture, which contained the radiolabeled fragment (86 fmol;
~280,000 cpm), competitor DNA (0.2 µg of sonicated salmon sperm
DNA/µl), and tracking dye (0.02% xylenecyanol FF) in 2× footprint
buffer (80 mM Tris-HCl [pH 7.2], 12 mM MgCl2, 2 mM dithiothreitol, 20% glycerol). The mixture was incubated for 20 min
at room temperature and subsequently loaded onto a 10% native
polyacrylamide gel (ratio of acrylamide to bisacrylamide, 75:1
[wt/wt]) with 0.5× TBE buffer (TBE buffer is 89 mM Tris base, 89 mM
boric acid, 2.5 mM EDTA; final pH 8.3) containing 20 µM cAMP as gel
and running buffer. Electrophoresis was carried out at a constant
voltage of 180 V and cooled with tap water. The gel was subsequently
dried and exposed to a phosphorimager screen (Molecular Dynamics).
The DNase I footprint assays with CRP and CitBHis
were carried out essentially as described for
CitBHis (24). Constant amounts of
the labeled 348-bp MluI-SphI DNA fragment
(~300,000 cpm) were incubated with CRP (final concentration, 3.7 or
2.0 µM) and phosphorylated CitBHis (final
concentration, 0.4 or 1.6 µM). CitBHis was
phosphorylated with ATP, and the kinase domain of CitA was fused to the
maltose binding protein (MalE-CitAC) as previously described (23,
24). The reaction mixtures contained CRP and/or
CitBHis, competitor DNA (20 ng of sonicated
salmon sperm DNA/µl), 1 mM cAMP, and the labeled DNA fragment in 1×
footprint buffer supplemented with 10 mM CaCl2
and 100 mM KCl. A total of 7.5 U of DNase I was added to start the
reaction. A control reaction was carried out with buffer instead of
protein solution. If no CRP was present in the reaction mixture, cAMP
was omitted. The samples were separated on a 6% denaturing
polyacrylamide gel containing 7 M urea.
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RESULTS |
Influence of preculture conditions on anaerobic growth with
citrate.
In a first set of experiments, we studied the effect of
the preculture conditions on the growth characteristics of K. pneumoniae during citrate fermentation. Precultures were grown
either anaerobically on citrate minimal medium or aerobically on
citrate or glucose minimal medium. Following inoculation with these
precultures, fermentative growth on citrate minimal medium started
after a lag phase of 0.5, 5, and 10 h, respectively (data not
shown). This result confirmed that the citrate fermentation enzymes are not constitutive but are induced under anoxic conditions in the presence of citrate. The reduced lag phase of cells precultured under
oxic conditions with citrate might be due to a slightly increased
concentration of the CitA-CitB two-component system, allowing for a
faster induction upon a shift to anoxic conditions. Comparable
induction patterns were previously reported for citrate fermentation by
Salmonella enterica serovar Typhimurium (45).
Influence of glucose, gluconate, and glycerol on anaerobic citrate
utilization.
To test the influence of glucose, gluconate, and
glycerol on citrate fermentation, different concentrations of these
carbon sources were added to citrate minimal medium before inoculation with a preculture grown anaerobically with citrate as the sole carbon and energy source. As shown in Fig.
2A, the presence of glucose led to
typical diauxic growth curves. The start of the intermediate lag phase
was strictly dependent on the glucose concentration, showing that
glucose is used preferentially to citrate. If gluconate was added
to citrate minimal medium, growth was also diauxic and showed
preferential use of gluconate. However, the diauxic effect was less
pronounced than with glucose (Fig. 2B). When glycerol was present in
addition to citrate, no diauxic growth was observed, but the growth
rate was slower than in the presence of either substrate alone (Fig.
2C).

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FIG. 2.
Anaerobic growth of the K. pneumoniae
wild type in citrate minimal medium containing different concentrations
of glucose (A), gluconate (B), and glycerol (C). The inoculating
culture had been grown anaerobically on citrate minimal medium. For the
sake of better readability, the individual growth curves are displayed
with time differences. Symbols indicate the presence of the following
concentrations of glucose, gluconate, or glycerol as noted above: (A)
solid circles, 8 mM; open circles, 4 mM; solid triangles, 2 mM; open
triangles, 1 mM; solid squares, 0 mM; (B) solid circles, 20 mM; open
circles, 8 mM; solid triangles, 4 mM; open triangles, 2 mM;
filled squares, 1 mM; (C) open triangles, 20 mM; solid triangles,
10 mM; open circles, 5 mM; solid circles, 0 mM. The solid squares in
panel C indicate the presence of glycerol minimal medium without
citrate.
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The data reported above clearly showed that citrate fermentation is
subject to catabolite repression. In several cases it was shown that
catabolite repression is due to direct inhibition of catabolic enzymes
by unphosphorylated enzyme IIAGlc, e.g., in the
case of lactose permease (26, 28) or glycerol kinase
(27). We therefore tested whether the addition of glucose, gluconate, or glycerol to citrate-fermenting cells inhibited the further catabolism of citrate. As shown in Fig.
3, the addition of the three
different carbon sources led to an only slightly reduced citrate
consumption, indicating that none of the proteins specifically involved in citrate fermentation, i.e., the
citrate carrier CitS, citrate lyase, and oxaloacetate
decarboxylase, is directly inhibited. The small reduction of citrate
consumption is probably due to reduced concentrations of these enzymes
as a consequence of reduced synthesis (see below).

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FIG. 3.
Anaerobic growth and citrate consumption of the
K. pneumoniae wild type in citrate minimal medium (solid
circles) or in citrate minimal medium with either 4 mM glucose (A), 4 mM gluconate (B), or 10 mM glycerol (C) (indicated in panels A through
C by open circles). The additional carbon sources were added at an
OD600 of about 0.15 (arrows).
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Influence of glucose, gluconate, and glycerol on
citS'-'lacZ
expression.
The above results indicated that catabolite repression
of citrate fermentation by glucose, gluconate, and glycerol was at the
level of enzyme synthesis. Therefore, the influence of the alternative
carbon sources on the expression of the citrate fermentation genes was
tested by adding them to a culture of K. pneumoniae strain
MB1 already growing exponentially on citrate minimal medium. This
strain carries a chromosomally integrated
citS'-'lacZ fusion (6), which served
as reporter for the determination of the expression of the
citS operon. As shown in Fig.
4B, addition of 4 mM glucose led to a
rapid decrease in
-galactosidase activity. Within 3 h, activity
dropped from 5,500 to 1,500 Miller units and increased again to
~4,000 Miller units when glucose had been consumed. Although less
pronounced, the growth curve was diauxic as in the experiment shown in
Fig. 2A. If glucose was added at a higher optical density
(OD600 > 0.15), the diauxic effect disappeared, possibly because all citrate had already been consumed when catabolite repression was relieved. In a control culture, where 4 mM citrate was
added instead of glucose,
-galactosidase activity constantly remained between 4,000 and 6,000 Miller units up to the end of growth
(Fig. 4A). When 4 mM gluconate was added as an additional carbon
source,
-galactosidase activity was reduced from 5,500 to 2,200 Miller units within 3 to 4 h and then increased again to 4,000 Miller units (Fig. 4C). Although there was no intermediate lag phase
visible in the growth curve, the increase in
-galactosidase activity
showed that gluconate had been consumed and catabolite repression had
been relieved. Similar to gluconate, addition of 10 mM glycerol led to
a decrease of
-galactosidase activity from 5,500 to about 2,000 Miller units within 3 h and then remained constant at this level
up to the end of growth (Fig. 4D). The lack of an increase in
-galactosidase activity in this experiment is due to the high
concentration of glycerol added, resulting in a complete consumption of
citrate before glycerol has been consumed. In summary, all carbon
sources tested reduced expression of the citS operon to
about 25 to 40% of the level measured in their absence.

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FIG. 4.
-Galactosidase activity in Miller units
(triangles) and OD600 (circles) of K.
pneumoniae strain MB1 during anaerobic growth in citrate
minimal medium with either 4 mM glucose (B), 4 mM gluconate
(C), or 10 mM glycerol (D) added at an OD600 of 0.1 (arrows). In a control culture (A), 4 mM citrate was added at an
OD600 of 0.1 (arrow).
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Independent evidence for the inhibition of expression of the citrate
fermentation genes by glycerol was obtained previously by Northern blot
experiments. The level of the transcripts of the citS operon
and of the citC operon in RNA isolated from cells grown
anaerobically with citrate and glycerol was significantly lower than in
RNA isolated from cells grown anaerobically with citrate as the sole
carbon and energy source (6, 24).
Influence of cAMP on diauxic growth.
The results described
above showed that the citrate fermentation genes are subject to
catabolite repression. Since in enterobacteria the CRP-cAMP system
plays a central role in catabolite repression and since three potential
CRP binding sites are present in the citC-citS intergenic
region, studies were performed to determine whether this system
also regulates expression of the K. pneumoniae citrate fermentation genes. First, the effect of exogenously added cAMP
on growth of the K. pneumoniae wild type in citrate minimal medium containing 2 mM glucose was tested. To this end, three cultures
were inoculated with a preculture grown anaerobically in citrate
minimal medium. To two of these cultures, cAMP (20 mM) was added at an
OD600 of 0.095 and 0.271, respectively, while the
third one served as control and received no cAMP (Fig.
5). Since 2 mM glucose supported growth
to an OD600 of approximately 0.4, cAMP addition
preceded glucose depletion. The addition of cAMP at an
OD600 of 0.271 clearly diminished the diauxic
effect observed in the control culture, indicating an enhanced
expression of the citrate fermentation genes prior to the complete
consumption of glucose. If cAMP was added at an
OD600 of 0.095, the diauxic effect was also
abolished, but in addition, the growth rate and the final cell density
were significantly reduced. The reason for this inhibition is unknown;
it may be caused by an interference of citrate fermentation and glucose
fermentation or by other components of the cAMP-CRP regulon.

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FIG. 5.
Influence of cAMP (20 mM) on growth of the K.
pneumoniae wild type in citrate minimal medium containing 2 mM
glucose. The addition of cAMP is indicated by solid symbols. For the
sake of better readability, the individual growth curves are displayed
with a time difference of 1 h.
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The cAMP effect and the presence of three putative CRP binding
sequences in the citC-citS intergenic region
(Fig. 1) indicated an involvement of CRP in catabolite repression of
the citrate fermentation genes. To demonstrate this, several attempts
were made to study the effect of a crp deletion on the
expression of the citrate fermentation genes. Unfortunately, our
efforts to construct a crp deletion mutant of the K. pneumoniae strain used in this study failed (data not shown).
Since we were not able to analyze the role of CRP in the expression of
the citrate fermentation genes in vivo, the ability of purified CRP to
bind to the potential binding sites in the
citC-citS promoter region was tested.
Purification of CRP from K. pneumoniae.
The
crp gene of K. pneumoniae ATCC 13882 was amplified by PCR from chromosomal DNA using Vent DNA
polymerase. The resulting 655-bp product was cloned into the
expression vector pET24b with the restriction sites that had been
introduced with the primers. Sequence analysis of two of the resulting
pET-CRP plasmids revealed two positions that differed from the
published sequence of K. aerogenes crp (29).
These differences did not cause a change at the protein level, however.
For CRP overproduction, pET-CRP was transferred into E. coli
BL21(DE3), which carries the gene for the T7 RNA polymerase under
the control of an IPTG-inducible lacUV5 promoter. After
induction with IPTG, a dominant protein band was observed after
SDS-PAGE of whole-cell extracts (Fig. 6).
Its apparent size of about 25 kDa corresponded well with the predicted
molecular mass of CRP (23.7 kDa). Fractionation of the cells revealed
that most of the protein was present in the supernatant obtained after
ultracentrifugation of cell extract, indicating that CRP had been
obtained in a soluble form. Purification of CRP was achieved by
affinity chromatography with cAMP agarose as a matrix. The eluted
protein was essentially pure as estimated by Coomassie-stained
polyacrylamide gels (Fig. 6). It should be mentioned that a very small
proportion of the purified protein was probably E. coli CRP,
which differs, however, from K. pneumoniae CRP in only one
position (29). The corresponding proteins were shown to be
completely interchangeable with respect to activation of the E. coli lacZ and the K. pneumoniae hutU promoters
(30).

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FIG. 6.
Coomassie-stained SDS-PAGE gel containing the following
samples: whole-cell lysate of E. coli BL21(DE3)/pET-CRP
prior to (lane 1) and 3 h after (lane 2) IPTG induction,
protein standards (lane 3), and purified CRP protein (lanes 4 and 5)
after affinity chromatography on cAMP agarose.
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Binding of CRP to the citC-citS intergenic
region.
Purified CRP was used for gel retardation assays with
radioactively labeled 348-bp MluI-SphI DNA
fragments encompassing the citC-citS intergenic region. As
shown in Fig. 7, two specific protein-DNA
complexes were observed, indicating that CRP was bound to two of three
putative binding sites present on this fragment. Half-maximal binding
required about 0.5 µM CRP. To define the CRP binding sites more
exactly, DNase I footprint experiments were performed with the same DNA
fragment used in the gel retardation assay. With CRP concentrations up
to 3.7 µM, hardly visible hypersensitive sites were present at
positions
35 and
46 upstream of the citC transcription
start site (Fig. 8, lane 5). When the
DNase I footprint experiment was performed with 2.0 µM CRP in the
presence of either 0.4 µM CitBHis or 1.6 µM
CitBHis (Fig. 8, lanes 6 and 7), the hypersensitive sites at positions
35 and
46 upstream of the citC transcription start site were easily visible; in
addition, a strong hypersensitive site at position
47 upstream of the
citS transcription start site appeared. Since none of the
hypersensitive sites was observed in DNase I footprints obtained with
CitBHis alone (Fig. 8, lanes 2 and 3), they must
be caused by the presence of CRP.

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FIG. 7.
Gel retardation assay with CRP and the 348-bp
MluI-SphI DNA fragment covering the
intergenic region between citC and citS.
The concentration of CRP is indicated on top of the figure.
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FIG. 8.
DNase I footprint assay with CRP and
CitBHis. The 348 bp MluI-SphI
fragment covering the citC-citS intergenic region was
labeled by fill-in of the 3'-recessed ends created by
MluI with Klenow polymerase. Lane 1, G+A sequencing
ladder; lane 2, 0.4 µM CitBHis; lane 3, 1.6 µM
CitBHis; lane 4, no protein; lane 5, 3.7 µM CRP; lane 6, 2.0 µM CRP plus 0.4 µM CitBHis; lane 7, 2.0 µM CRP
plus 1.6 µM CitBHis. The hypersensitive sites (indicated
with asterisks) are located at positions 47 relative to the
citS transcription start site (top) and at 35 and 46
relative to the citC transcription start site
(bottom).
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The location of the hypersensitive sites strongly indicated that CRP
binds to the two postulated sites centered at
41.5 upstream of the
citC and citS transcription start sites, but not
to the one in between. This is in accord with the result of the gel
retardation assay, which indicated two CRP binding sites to be present
in the citC-citS intergenic region, and with the fact that
the putative CRP binding site, which is not occupied, strongly overlaps
with the CitB binding site (Fig. 1). The influence of
CitBHis on the appearance of the hypersensitive
sites indicated that CRP binding is stimulated by
CitBHis, in particular to the site in front of the citS promoter.
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DISCUSSION |
Catabolite repression has been studied extensively in
enterobacteria, in particular in E. coli, during the
last decades. Nearly all studies have focused exclusively on
catabolite repression during aerobic growth. The results reported in
this study provide an example of catabolite repression under
anaerobic, fermentative conditions. Three different carbon
sources, i.e., glucose, gluconate, and glycerol, taken up by
fundamentally different transport systems and metabolized by different
pathways, were shown to inhibit the expression of the citrate
fermentation genes. The strongest repression was exerted by glucose and
resulted in typical diauxic growth curves (Fig. 2A). The repression by
gluconate was weaker, but still led to diauxie (Fig. 2B). The
repressing effect of glycerol was in the same range as that of
gluconate, but in this case, no diauxie was observed (Fig. 2C). In
enterobacteria, catabolite repression is prevalently exerted by the
cAMP-CRP complex and we provide evidence that this holds true also for
the citrate fermentation genes in K. pneumoniae. First, the
diauxic effect caused by glucose could be impaired by addition of cAMP;
second, CRP was shown to bind to two sites in the citC-citS
intergenic region, which are centered at
41.5 upstream of the
citC and the citS transcription start sites. This
position was previously demonstrated to be one of the optimal sites for
transcriptional activation by the cAMP-CRP complex (15).
Interestingly, the binding of the cAMP-CRP complex was easily observed
in a gel retardation assay, whereas the emergence of hypersensitive
sites in DNase I footprints was extremely weak with the cAMP-CRP
complex alone but strongly supported by the simultaneous presence of
the response regulator CitB. The latter observation indicated that
binding of the cAMP-CRP complex to the citC-citS intergenic
region is stimulated by the previous binding of phosphorylated CitB
(24). Since the expression of the citrate fermentation
genes was only partially inhibited by the alternative carbon sources
(Fig. 4), it seems possible that the cAMP-CRP complex serves to enhance a basal, CitB-dependent transcription level in the absence of repressing carbon sources. Since the citAB genes are
positively autoregulated by cotranscription with citS and
oadGAB (6), a reduced transcription of the
citS operon due to a low cAMP-CRP concentration would result
in lowered levels not only of the dissimilatory proteins (CitS and
oxaloacetate decarboxylase) but also of the regulatory proteins CitA
and CitB. As a consequence, transcription of the citrate fermentation
genes will decrease even further.
The mechanism described above implies that the repressing carbon
sources reduce the cAMP-CRP concentration. It was recently shown that
not only glucose and other PTS sugars, but also non-PTS substrates such
as lactose or gluconate, in fact lead to lower levels of both cAMP and
CRP (17). In the case of cAMP, it is believed that enzyme
IIAGlc, a protein of the PTS and a key player in
catabolite repression of enterobacteria (33), activates
adenylate cyclase, the cAMP biosynthetic enzyme, when it is present in
the phosphorylated state. PTS substrates cause dephosphorylation of
enzyme IIAGlc mainly by phosphoryl transfer to the
sugars, whereas non-PTS sugars can elicit dephosphorylation of
IIAGlc by a reduction of the PEP/pyruvate ratio
(16). For gluconate, however, it was shown that despite a
lowered PEP/pyruvate ratio, enzyme IIAGlc was
predominantly in the phosphorylated state (16).
Therefore, another mechanism seems to be effective for the
gluconate-induced reduction of the cAMP level. The lowering of the CRP
concentration in the presence of repressing carbon sources seems to be
due to complex autoregulation of the crp gene (18, 19,
40).
Based on the findings described above, a reduced concentration of the
cAMP-CRP complex is also postulated to be the cause of catabolite
repression by glucose, gluconate, and glycerol during citrate
fermentation in K. pneumoniae. However, further experiments are required to prove this hypothesis, such as measurements of the
concentrations of cAMP, CRP, PEP, and pyruvate and of the phosphorylation state of enzyme IIAGlc under the
fermentative conditions used in our studies. As the fermentation of
glucose, gluconate, and glycerol involves the formation of pyruvate
from PEP, it seems likely that these carbon sources lead to a different
PEP/pyruvate ratio than fermentation of citrate, where pyruvate is
formed from oxaloacetate and PEP required for biosynthetic purposes has
to be generated from pyruvate by PEP synthetase. Irrespective of the
outcome of such studies, the data provided here and by others (8,
35) show that the sophisticated mechanism of CRP-mediated
catabolite repression in enterobacteria works not only under
aerobic but also under anaerobic, fermentative conditions.
This work was supported by a grant from the Swiss National
Foundation for Scientific Research to M.B.
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