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Journal of Bacteriology, April 2001, p. 2497-2504, Vol. 183, No. 8
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.8.2497-2504.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Regulation of the Acetoin Catabolic Pathway Is
Controlled by Sigma L in Bacillus subtilis
Naima
Ould Ali,
Joelle
Bignon,
Georges
Rapoport, and
Michel
Debarbouille*
Unité de Biochimie Microbienne,
Institut Pasteur, URA 2172 du Centre National de la Recherche
Scientifique, 75724 Paris Cedex 15, France
Received 22 September 2000/Accepted 23 January 2001
 |
ABSTRACT |
Bacillus subtilis grown in media containing amino acids
or glucose secretes acetate, pyruvate, and large quantities of acetoin into the growth medium. Acetoin can be reused by the bacteria during
stationary phase when other carbon sources have been depleted. The
acoABCL operon encodes the E1
, E1
, E2, and E3
subunits of the acetoin dehydrogenase complex in B. subtilis. Expression of this operon is induced by acetoin and
repressed by glucose in the growth medium. The acoR gene is
located downstream from the acoABCL operon and encodes a
positive regulator which stimulates the transcription of the operon.
The product of acoR has similarities to transcriptional
activators of sigma 54-dependent promoters. The four genes of the
operon are transcribed from a
12,
24 promoter, and transcription is
abolished in acoR and sigL mutants. Deletion analysis showed that DNA sequences more than 85 bp upstream from the
transcriptional start site are necessary for full induction of the
operon. These upstream activating sequences are probably the targets of
AcoR. Analysis of an acoR'-'lacZ strain of
B. subtilis showed that the expression of acoR
is not induced by acetoin and is repressed by the presence of glucose
in the growth medium. Transcription of acoR is also
negatively controlled by CcpA, a global regulator of carbon catabolite
repression. A specific interaction of CcpA in the upstream region of
acoR was demonstrated by DNase I footprinting experiments,
suggesting that repression of transcription of acoR is
mediated by the binding of CcpA to the promoter region of
acoR.
 |
INTRODUCTION |
During the growth of cultures of
Bacillus subtilis, several products have been identified in
the growth medium, such as lactate, acetate, succinate, acetoin,
butanediol, and ethanol (5).
Acetoin (3-hydroxy 2-butanone) is a major catabolic product of B. subtilis grown aerobically in glucose media. Since it is neutral,
this metabolite allows the bacteria to degrade large amounts of glucose
without substantial acidification of the growth medium. Acetoin also
serves as a carbon storage compound which is secreted into the growth
medium and later reimported. In B. subtilis, the products of
two genes, ilvBN (acetohydroxy acid synthase) and
alsS (
-acetolactate synthase), are involved in the
production of acetolactate from pyruvate. Acetolactate is converted to
acetoin by spontaneous decarboxylation at low pH or via the action of
alsD, encoding an acetolactate decarboxylase (37). Acetoin is reutilized during stationary phase when
other carbon sources have been depleted. Many bacterial species are able to degrade acetoin: Micrococcus urea (20),
Alcaligenes eutrophus (12), Enterococcus
faecalis (10), Pelobacter carbinolicus (34), Klebsiella pneumoniae (9),
and Clostridium magnum (22). Three genes
forming an operon, acuABC, have been described in B. subtilis. The roles of the corresponding gene products are still
unknown (16). Inactivation of the first gene of this
operon resulted in diminished growth on acetoin and butanediol. Since utilization of acetoin is reduced but not abolished in an
acuABC mutant, this result suggested that there is more than
one pathway for acetoin utilization in B. subtilis.
Recently, another gene cluster, the aco operon encoding the
multicomponent acetoin dehydrogenase enzyme complex, was sequenced
(18, 23). A plasmid encoding part of the
subunit of
the acetoin dehydrogenase E1 was used to disrupt acoA, the
first gene of this operon. This mutant was impaired in the expression
of acetoin dehydrogenase E1 activity and for depletion of acetoin from
the growth medium, indicating that this operon is the main system
involved in the catabolism of acetoin (18). However, very
little was known about the regulation of transcription of the
aco operon in B. subtilis. The product of the
acoR gene, which is located downstream from the
aco operon, has similarities to transcriptional activators
of sigma 54-dependent promoters. A putative
12,
24 promoter is
located upstream from the acoA gene, strongly suggesting
that the SigL sigma factor is necessary for its transcription. We
studied the regulation of the expression of the aco operon
in B. subtilis and found that transcription was strongly
induced in the presence of acetoin in the growth medium and depended
upon the presence of both AcoR and SigL.
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MATERIALS AND METHODS |
Bacterial strains and culture media.
The B. subtilis strains used in this work are listed in Table
1. Escherichia coli TGI [K-12
(lac pro) supE thi hsd5/F' traD36 proA+B+
laclq lacZ
M15] was used for
cloning experiments. E. coli was grown in Luria-Bertani
broth (38), and B. subtilis was grown in SP medium (8 g/liter of nutrient broth [Difco], 1 mM MgSO4,
10 mM KCl, 0.5 mM CaCl2, 10 µM MnCl2, 2 µM
FeSO4) or in CSK medium. CSK medium is C medium
(28) supplemented with potassium succinate (6 g/liter) and
potassium glutamate (8 g/liter).
Transformation and phenotype characterization.
Standard
procedures were used to transform E. coli (38),
and transformants were selected on Luria-Bertani broth plates
containing ampicillin (100 µg/ml). B. subtilis was
transformed with plasmid or chromosomal DNA as previously described
(1, 28), and transformants were selected on SP medium
plates containing chloramphenicol (5 µg/ml), kanamycin (5 µg/ml),
erythromycin (1 µg/ml) plus lincomycin (25 µg/ml), or spectinomycin
(60 µg/ml). Amylase activity in B. subtilis was detected
after growth on tryptose blood agar base (Difco) containing 10 g
of hydrolyzed starch per liter (Connaught). Starch degradation was
detected by sublimating iodine onto the plates.
DNA manipulations.
Standard procedures were used to extract
plasmids from E. coli (38). Restriction
enzymes, phage T4 DNA polymerase, phage T4 DNA ligase, and phage T4
polynucleotide kinase were used as recommended by the manufacturers.
DNA fragments were purified from agarose gels with a Prep-A-Gene kit
(Bio-Rad Laboratories). The PCR technique with Thermus
aquaticus DNA polymerase was used for amplification. The
oligonucleotide primers used included mismatches to create restriction sites.
Plasmid constructions.
pAC5 (29), a derivative
of pAF1 (11), carries the pC194 chloramphenicol resistance
gene cat and a lacZ gene between two fragments of
the B. subtilis amyE gene. PCR was used to introduce EcoRI restriction sites at various positions upstream from
acoA. PCR was performed with one oligonucleotide
(5'-GGAGGATCCTCAGTTAATGACAAGCCTTC-3') corresponding to the
coding sequence of the acoA gene (codons 7 to 13) and one
oligonucleotide corresponding to various positions in the
acoA promoter region. The EcoRI-BamHI
restriction fragments generated were inserted between the
EcoRI and BamHI restriction sites of pAC5,
creating translational fusions between codon 13 of acoA and
codon 8 of lacZ. The DNA sequences of the different PCR
fragments were verified by direct sequencing of the various corresponding plasmids. The resulting plasmids were linearized at the
single PstI restriction site and integrated into the
chromosome of strain 168 by homologous recombination at the
amyE locus using chloramphenicol selection. The integrants
carrying the translational fusions were named QB7700, QB7719, QB7720,
and QB7721.
Gene disruptions and transcriptional fusions with pMutin4
(
40) were constructed by PCR amplification of an internal
segment
of the target gene, ligation of the amplified DNA fragment into
pMutin4, transformation of
E. coli, and then insertion of
the
plasmid into the
B. subtilis chromosome. The following
oligonucleotides
were used for PCR amplifications:
5'-GCCGAAGCTTGCCCAGGGAGTGCTTCCC-3'
and
5'-CGCGGATCCAGCAGCCGCCCGATCGGC-3' for the
acoA
gene, 5'-GCCGAAGCTTGTCGCCGGGGGAGCGGCG-3'
and
5'-CGCGGATCCGACCTGCTTGCCGACTGC-3' for the
acoB
gene, 5'-GCCGAAGCTTGGCGGTAAAAGTAGTGATG-3'
and
5'-CGCGGATCCGATCGTCAGCTGCGCGC-3' for the
acoC
gene, and 5'-GCCGAAGCTTGACCGGCTGATCCCGGCT-3'
and
5'-CGCGGATCCGCCGATCTTCACATCCCC-3' for the
acoL
gene. The target
genes were interrupted by Campbell-type crossover
integration.
The integration of the recombinant plasmids fuses the
target genes
to the
lacZ gene, leading to a transcriptional
fusion.
The wild-type
acoR gene was disrupted as follows. Two DNA
fragments encoding the amino-terminal and the carboxy-terminal parts
of
acoR were synthesized by PCR with the following pairs of
oligonucleotides,
respectively: (i)
5'-GAAGAATTCGAAGGGGCATGCTGGACAGAAAC-3' and
5'-GGAGGATCCCTGCCAATCCGGCATTGAGGTTC-3'
and (ii)
5'-CTGCTGCAGCGCGATCGCACCGAGGATATCCC-3' and
5'-AAGAAGCTTTCCAGCGGCTTCCAGTAAAGCGG-3'
. The two DNA
fragments were ligated into pHT181 (
25) on each
side of a
DNA fragment containing
aphA3 (
39), leading to
pACOR2.
The interrupted gene was introduced into the chromosome of
strain
QB7700 to give strain QB7704. The wild-type
acoR gene
was cloned
as follows. Strain QB7704 was transformed with a library of
B. subtilis DNA established in
E. coli by using
the shuttle vector
pHT315 (
24). Transformants were
isolated on CSK-erythromycin
plates containing 10 mM acetoin and X-Gal
(5-bromo-4-chloro-3-indolyl-

-
D-galactopyranoside).
Several blue colonies were isolated. Plasmid DNA was extracted
from
cultures of one of these transformants, and the insert was
characterized by DNA sequencing. The corresponding plasmid, which
contained the entire wild-type
acoR gene, was called
pACOR1.
An
acoR'-'
lacZ transcriptional fusion was
constructed in pDIA5307 (
4) by PCR amplification of an
internal fragment of the
acoR gene, ligation of the
amplified DNA fragment into pDIA5307,
transformation of
E. coli, and insertion of the recombinant plasmid
into the chromosome
of the 168 strain of
B. subtilis, leading
to strain QB7713.
PCR amplification was done with two oligonucleotides:
5'-GAAGAATTCGAAGGGGCATGCTGGACAGAAAC-3' and
5'-GGAGGATCCCTGCCAATCCGGCATTGAGGTTC-3'
.
Reverse transcriptase mapping of the mRNA start point in the
acoA gene.
Total RNA was isolated from B. subtilis 168 grown in CSK medium with or without 10 mM acetoin as
the inducer. Exponentially grown cells were harvested at an optical
density at 600 nm of 0.5, and RNA was extracted (15). One
oligonucleotide (5'-CCTCAGTTAATGACAAGCCTTCTCG-3') complementary to the acoA coding sequence was labeled
with 10 U of polynucleotide kinase and 0.37 MBq of
[
32P]ATP (15 TBq/mmol; Amersham). The DNA primer was
elongated, and the product was analyzed as previously described
(27).
DNase I footprinting.
DNA fragments used for DNase I
footprinting were prepared by PCR using Pfu polymerase
(Stratagene) and 20 pmol of each primer (5'-GGCGCTGTTAAGCACGATCGGCCTTGCG-3' and
5'-CCGTTTTCTTAATCGGGCTTCGTCAACC-3' ), one of which was
previously labeled with T4 polynucleotide kinase (New England Biolabs)
and [
32P]ATP. The labeled PCR products were purified
with the Qiagen PCR purification kit. Binding of CcpA, HPr, or
HPr-Ser-P to these DNA probes was performed in a 20-µl volume
containing 2 × 105 cpm of the 32P-labeled
DNA fragments and 1 µg of poly(dI-dC) in 100 mM KCl, 10 mM HEPES (pH
7.6), 0.1 mM EDTA, 2 mM MgCl2, 1 mM dithiothreitol, and
10% glycerol. The DNA binding reaction was performed in the presence
of 2 µM CcpA and 10 µM either HPr or HPr-Ser-P by incubating the
assay mixture for 45 min at room temperature. The concentrations of
MgCl2 and CaCl2 were adjusted to 1 and 0.5 mM,
respectively, and 20 ng of DNase I (Worthington Biochemical, Freehold,
N.J.) was added. The mixture was incubated at room temperature for 1 min, and the reaction was stopped by the addition of 7 volumes of stop
buffer (0.4 M sodium acetate, 50 µg of calf thymus DNA/ml, 2.5 mM
EDTA) followed by phenol extraction. The DNA fragments were ethanol
precipitated, and an equivalent number of cpm (2 × 105) from each reaction was loaded on 7% polyacrylamide
sequencing gels. A+G Maxam and Gilbert reactions (32) were
carried out on the appropriate 32P-labeled DNA fragments,
and the products were loaded alongside the DNase I footprinting
reactions. Gels were dried and analyzed by autoradiography.
-Galactosidase assays.
B. subtilis cells
containing lacZ fusions were grown to an optical density at
600 nm of 1.
-Galactosidase specific activities were determined as
previously described and are expressed as Miller units per milligram of
protein (7). The values reported are averages of at least
three independent assays.
Acetoin assays.
The acetoin assays were carried out as
previously described (16) except that the reactions were
done at room temperature for 15 min.
Glucose assays.
The glucose assays were performed by an
enzymatic method using glucose oxidase and peroxidase as recommended by
the manufacturer (Boehringer).
 |
RESULTS |
Induction of the aco operon in response to acetoin or
glucose availability.
Four genes which probably form an operon
encode the E1
, E1
, E2, and E3 subunits of the acetoin
dehydrogenase multienzyme complex (18). It was previously
shown that utilization of acetoin strongly depends upon the culture
conditions. Addition of acetoin led to an increase in the specific
activity of acetoin dehydrogenase, whereas addition of acetoin with
glucose prevents this increase. An acoA'-'lacZ
translational fusion was constructed and used to elucidate the
regulation of the expression of the aco operon. The
expression of the hybrid gene was studied in strain QB7700 grown in
minimal CSK medium with and without 10 mM acetoin as the inducer.
lacZ expression was strongly induced by acetoin in the
growth medium, as shown in Table 2. The
acuABC gene cluster plays a role in acetoin catabolism. The
product of acuC shares similarities with eukaryotic histone
deacetylase (16). In eukaryotes, histone deacetylation
plays an important role in transcriptional regulation of cell cycle
progression and developmental events. We constructed a strain in which
the acuABC operon was deleted. The mutation was introduced
by transformation into QB7700, leading to strain QB7728. We did not
observe any modification of the induction of the
acoA'-'lacZ fusion, and the repression effect
observed in the presence of glucose was similar to that observed in the parental strain QB7700 (not shown). This indicates that the
acu operon has no effect on the expression of the
aco operon in B. subtilis. Addition of glucose
repressed the expression of the lacZ fusion. CcpA, a member
of the LacI-GalR family of repressors, is a regulator of catabolite
repression in B. subtilis. It is a negative regulator of
carbon utilization genes and is a positive effector of genes involved
in the biosynthesis and secretion of acetate and acetoin (17,
19). The role of CcpA in glucose control was investigated by
testing the effect of a
ccpA mutation on the regulation
of the aco operon. Chromosomal DNA from strain QB5407
ccpA::spc was introduced by
transformation into strain QB7700, leading to strain QB7701. The effect
of glucose was tested by comparing the
-galactosidase activity after
the growth of strain QB7701 in CSK acetoin medium and in CSK acetoin
glucose medium (Table 2). The expression of the
acoA'-'lacZ fusion remained inducible by acetoin
but was not repressed by glucose in the absence of CcpA in the cell.
It was previously shown that different carbon sources influence the
ability of
B. subtilis to degrade acetoin (
26).
To assess
the relationships among acetoin production, glucose
degradation,
and induction of the
aco operon, strain QB7700
was grown in CSK
medium containing 42 mM glucose. Glucose, acetoin, and
lacZ were
assayed at various times for 24 h (Fig.
1). During the exponential
phase of
growth, the glucose concentration decreased rapidly while
acetoin
production increased to 35 mM, indicating that most of
the glucose was
converted to acetoin in the culture medium. As
expected, the acetoin
concentration began to decline when glucose
was completely metabolized.
In parallel, the
acoA'-'
lacZ fusion
present in
the QB7700 strain was induced, indicating that acetoin
produced during
aerobic growth in the presence of glucose induced
the
aco
operon. Strikingly, the complete disappearance of glucose
from the
medium marked the start of transcription of the
aco operon.

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FIG. 1.
Induction of the acoA'-'lacZ
fusion after growth in glucose medium. B. subtilis strain
QB7700 was cultured in CSK medium containing 42 mM glucose at 37°C.
The optical density of the culture, at 600 nm (OD 600) was followed for
24 h, and the glucose and acetoin concentrations and LacZ activity
were assayed. , optical density at 600 nm; , glucose
concentration; , acetoin concentration; , -galactosidase
specific activity.
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Induction of expression of acoABCL genes.
The
plasmid pMutin4 was used to construct transcriptional fusions with the
lacZ gene. Integration of pMutin4 fuses the target genes to
the lacZ gene and allows the expression of downstream genes
from an IPTG-inducible promoter, pspac. These fusions were integrated by homologous recombination into the acoABCL
genes in the chromosome, leading to strains QB7724, QB7725, QB7726, and
QB7727, respectively. The recombination events were mediated by DNA
fragments generated by PCR and corresponding to internal parts of each
gene. These events inactivated the corresponding genes and fused them
to the lacZ gene. The
-galactosidase activities of
strains QB7724, QB7725, QB7726, and QB7727 were assayed after they were
cultured in CSK medium containing or not containing acetoin (Table 2).
The presence of 10 mM acetoin led to 10- to 100-fold-higher
lacZ expression than in its absence. The induction by
acetoin indicates that these four genes are coexpressed and probably
belong to the same transcriptional unit. The level of
-galactosidase
expression in strains containing transcriptional fusions constructed
with pMutin4 was lower than that of the
acoA'-'lacZ translational fusion in the vector
pAC5. This is probably due to better translation of the
acoA'-'lacZ mRNA. The acoR gene is located immediately downstream from the aco operon. Addition
of 1 mM IPTG to the growth media of strains QB7724 and QB7727 did not
change the lacZ expression (not shown). This result
indicates that the expression of the acoR gene is not
affected by the pspac promoter inserted into the
acoA or acoL gene. This could be due to premature
termination of transcription initiated at the pspac promoter, suggesting that the aco operon and the
acoR genes are distinct transcriptional units.
The acoR and sigL gene products are
involved in aco expression.
The four genes,
acoABCL, of the operon are followed by acoR, a
gene which encodes a peptide of 67 kDa with similarities to activators
of sigma 54-dependent promoters. This family of activators contains a
region of 220 to 240 residues called the central domain, which is
specifically required for the formation of open complexes between RNA
polymerase and the
12,
24 promoters, probably by interacting with
the RNA polymerase or with sigma 54. An aphA3 cassette was
inserted into the acoR gene by a double-crossover event.
This mutation, which inactivates the acoR gene, was
introduced into the chromosome of QB7700, leading to strain QB7704.
-Galactosidase activity was assayed in QB7704 cultures in CSK medium
with or without acetoin and glucose (Table 2). The product of
acoR was found to be necessary for the expression of the
operon. This strongly suggests that the promoter of the aco
operon is recognized by an RNA polymerase associated with the SigL
sigma factor. Therefore, a sigL::aphA3
null mutation was introduced by transformation into QB7700, leading to
strain QB7702. The
-galactosidase activity was assayed in cultures
of this strain grown in CSK medium with or without acetoin as the
inducer (Table 2). There was no LacZ activity, indicating that a
SigL-dependent promoter is involved in the transcription of the
aco operon.
Promoter and control regions located upstream from the
acoABCL operon.
In gram-negative and gram-positive
bacteria, all promoters recognized by holoenzyme containing
54 possess at least one conserved GG doublet around
position
26 followed by a GC doublet at a distance of 10 bp (2,
33). The transcription start site of acoABCL was
mapped by primer extension using reverse transcriptase (Fig.
2). RNA was extracted from uninduced cells grown in CSK medium or induced cells grown in CSK medium containing 10 mM acetoin. A unique band was observed when RNA extracted
under induced conditions was used, allowing the definition of the
promoter. An alignment of the deduced promoter region with five other
12,
24 SigL-dependent promoters from B. subtilis is
shown in Fig. 3. The promoter contains
12 and
24 regions identical to those observed in sigma 54-dependent
promoters, for instance, the levanase and rocABC promoters
(4, 6). A second DNA sequence with similarities to the
12,
24 promoter is present 135 bp upstream from the transcription
start site. A DNA fragment lacking this similar sequence was
synthesized by PCR and fused upstream from the lacZ gene.
This construction was reintroduced at the amyE locus of
B. subtilis by using the plasmid pDH32 (35). The resulting strain did not express LacZ activity in CSK medium containing acetoin as the inducer (not shown). This result indicates that only one
12,
24 promoter identified by primer extension (shown
in Fig. 2) is involved in the transcription of the acoABCL operon.

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FIG. 2.
Reverse transcriptase mapping of the transcriptional
start site of the acoA gene. RNA was extracted from B. subtilis 168 grown in the presence (+ acetoin) or absence of 10 mM
acetoin. The position of the cDNA-extended fragment was compared to
that of fragments obtained by sequencing an M13 recombinant phage
containing the promoter region, with the same oligonucleotide used as a
primer. The transcriptional start site is indicated by an arrow.
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FIG. 3.
Nucleotide sequences of promoter regions of the
acoABCL operon (pacoA), the levanase operon
(plev) (6), the rocABC operon
(procABC) (4), the rocG gene
(procG) (3), the rocDEF operon
(procDEF) (14), and the bkd operon
(pbkd) (8). The transcriptional start sites are
indicated by arrows. The boxes indicate conserved DNA sequences around
positions 12 and 24 with respect to the transcriptional start
sites.
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The aco operon requires upstream sequences for its
expression.
Central-domain activators contact
54-holoenzyme through DNA looping after binding to the
enhancer, also called upstream activating sequences (UAS), typically 80 to 60 bp upstream from the transcription start site. A notable
exception is rocG in B. subtilis, which is
transcribed by a SigL-containing RNA polymerase and requires RocR, a
member of the NtrC/NifA family of proteins. Unlike other
54-dependent genes, rocG has no UAS; instead,
its expression is dependent on a sequence called DAS (downstream
activating sequence) located downstream from the rocG coding
region. This DAS also serves as a UAS for rocABC
(3). To identify any such sequences associated with
acoA expression, deletions ending upstream from the
transcriptional start site were introduced. A set of DNA fragments from
which part of the upstream region was missing was obtained by PCR
synthesis (see Materials and Methods). These fragments were then
inserted upstream from the lacZ gene in pAC5. The deletion end points are indicated in Fig. 4. The
fusions were reintroduced as single copies at the amyE locus
of B. subtilis. The levels of lacZ expression in
this strain were analyzed and are shown in Fig. 4. In the
B and
C
deletions, lacZ expression was identical to that obtained in
QB7700. In the
D deletion, lacZ expression was strongly
reduced, indicating that full induction of the aco operon
requires DNA sequences located between positions
123 and
85.
Interestingly, this DNA region includes three copies of a hexanucleotide sequence, 5'-GAGACA-3' , and also a
palindromic sequence of 11 bp centered on position
91. Possibly these
direct repeats or the palindromic sequence are involved in the binding of AcoR.

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FIG. 4.
Nucleotide sequence of the acoA upstream
region. The deletion end points are indicated by bent arrows and
numbered with respect to the transcriptional start site, labeled with
an asterisk. 12, 24 sequences are indicated. The boldly underlined
regions indicate putative palindromic UAS. The effects of upstream
deletions on expression of the acoA'-'lacZ
translational fusion are indicated on the right. -Galactosidase
specific activity was determined in extracts prepared from
exponentially growing cells in CSK medium containing 10 mM acetoin as
the inducer.
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Analysis of acoR gene expression.
The intergenic
region located between the end of acoL and the beginning of
acoR is 118 bp long, suggesting that acoR may be part of the acoABCL operon. This possibility was tested by
constructing a B. subtilis strain in which the
lacZ gene was integrated and fused into the acoR
gene. A DNA fragment encoding an internal part of acoR was
obtained by PCR synthesis and inserted into pDIA5307 upstream from the
lacZ gene. The recombinant plasmid was integrated by a
single-crossover event into the chromosome of strain 168, leading to
strain QB7713. As the integration of the lacZ gene inactivates the acoR gene, the plasmid pACOR1, which
contains the wild-type acoR, was introduced by
transformation into strain QB7713, leading to strain QB7714. The level
of lacZ expression was assayed in extracts of cultures of
strains QB7714 and QB7713 grown in CSK medium containing 10 mM acetoin
(Table 2). The results indicate that the transcription of
acoR was not induced by acetoin and did not require the
wild-type acoR gene for its expression. Therefore, the
acoR gene and the acoABCL operon are organized as
two distinct transcriptional units and acoR is not
autoregulated. In addition, the transcription of acoR is
strongly repressed by the presence of glucose in the growth medium. A
ccpA::spc null mutation was
introduced by transformation into strain QB7714, leading to strain
QB7733 (Table 1). The properties of this strain show that the
repression by glucose of the acoR transcription depended
upon CcpA (Table 2).
Catabolite repression of aco operon expression.
The acoABCL operon of B. subtilis is subject to
carbon catabolite repression by glucose via CcpA (Table 2).
Several CRE-like sequences could be involved in carbon catabolite
repression by glucose. A DNA sequence,
5'-TGATTTTACGGGCTCA-3', is located between positions
34 and
49 from the transcription start site of the acoABCL operon. Another DNA sequence,
5'-TGAATTCGGTCCCA-3', is located in the beginning of the
coding sequence of acoR (codons 1 to 5). Mutants were
constructed containing either point mutations or deletions of these
CRE-like sequences. The glucose effect in the resulting strains was
assayed and indicated that neither CRE-like sequence is involved in
catabolite control by glucose (not shown). Two other CRE-like sequences
are located in the intergenic region between acoL and
acoR (Fig. 5). In order to
test the binding of CcpA in the upstream region of acoR,
DNase I footprinting experiments were performed. A 239-bp DNA fragment
containing both CRE-like sequences located between the end of
acoL and the beginning of acoR was used as a
template. The results of the DNase I footprinting experiments are
presented in Fig. 6. In the presence of
CcpA, a clear protection pattern was observed in a single region
extending from 45 to 71 bases upstream from the ATG start codon of
acoR. A specific interaction between CcpA and HPr-Ser-P has
been demonstrated by several in vitro techniques (19).
Sites of hypersensitivity to DNase I digestion were observed when CcpA
and HPr-Ser-P were present in the reaction mixture. Similar alterations
of the pattern of DNase I digestion were previously observed outside
the CRE sequence in other systems (31).

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FIG. 5.
Organization of the acoR promoter region. The
DNA sequence located between the end of acoL and the
beginning of acoR is shown. DNA regions with similarities to
the CRE consensus sequence are underlined. Putative 10 and 35
regions of the acoR promoter are indicated in boldface
letters. Regions protected by CcpA are marked by brackets.
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FIG. 6.
DNase I footprinting analysis of CcpA binding to the
acoR promoter region. Lanes containing 2 × 105 cpm of the labeled nontemplate strand (A) and template
strand (B) of acoR are shown. Fragments were incubated in
the presence of 2 µM purified CcpA. A + G Maxam and Gilbert
reaction products of the appropriate DNA fragments were loaded in lanes
1. Lanes 2 through 5 were as follows: lanes 2, no protein; lanes 3, 2 µM CcpA; lanes 4, 2 µM CcpA and 10 µM HPr; and lanes 5, 2 µM
CcpA and 10 µM HPr-Ser-P. Regions protected by CcpA are indicated by
DNA sequences.
|
|
 |
DISCUSSION |
B. subtilis cells growing in medium containing an
excess of carbon source excrete a large number of organic compounds,
including pyruvate, succinate, acetate, and acetoin. It was previously
proposed that the conversion of pyruvate to acetoin or butanediol
prevents overacidification of the growth medium during exponential
growth (16). Acetoin is secreted during the exponential
growth phase and also serves as a carbon storage compound which can be
reused when other carbon sources have been exhausted. It is interesting to note that the CcpA protein is required for the expression of the
als gene, involved in the biosynthesis of acetoin, and of the ack and pta genes, which are involved in the
production of acetate. Conversely, CcpA is a repressor of the
transcription of the acu and aco operons.
B. subtilis therefore has a fine-tuning system controlling
both the synthesis and the degradation of secondary metabolites, such
as acetate and acetoin. We studied the regulation of transcription of
the aco operon. It contains four genes, acoABCL, encoding the acetoin dehydrogenase complex. Transcription of this operon is strongly induced in the presence of acetoin in the growth medium. A regulatory gene, called acoR, is required for the
positive regulation of this operon. This gene encodes a positive
regulator containing a central domain which is probably involved in the activation of the
12,
24 promoter. In this family of
transcriptional activators, there are several domains with different
functions. Typically, the amino-terminal domain is the signal reception
domain. The amino-terminal part of AcoR is a large domain of 300 residues, a characteristic which is shared with AcoR from A. eutrophus (21) and BkdR from B. subtilis
(8). This amino-terminal domain is probably involved in
the control of AcoR activity in response to the presence of the
internal inducer. We also characterized a DNA sequence located between
positions
85 and
123 with respect to the acoA
transcription start site and demonstrated that it is involved in the
transcription of the gene. This sequence contains a perfect palindromic
structure of 2 × 11 bp. Since the upstream part of the
palindromic structure is located between the deletion
C and the
deletion
D, it is tempting to speculate that this sequence is the
target of AcoR. Glucose represses the transcription of the
aco operon, and this catabolic control depends upon the catabolite control protein A (CcpA). CcpA is a pleiotropic repressor and binds to cis-active operator sequences. An interaction
of HPr-Ser-P with CcpA has been demonstrated in vitro, and the
resulting complex binds specifically to the CRE sequence in several
genes of B. subtilis. In addition to HPr, an HPr-like
protein, Crh, exhibiting 45% identity with HPr, participates in
catabolite repression (13). A DNA sequence located between
positions
50 and
38 in the promoter of the levanase operon shows
similarities to the CRE sequence. This sequence plays a role in
catabolite repression of the lev operon (30,
31). Interestingly, there is a similar DNA sequence at
approximately the same position in the promoter region of
acoA. Point mutations introduced by site-directed
mutagenesis did not affect repression by glucose. The transcription of
acoR itself is repressed by glucose, and a DNA sequence
located upstream from the start codon of acoR is protected
by CcpA against DNase I digestion. This protected region contains the
sequence 5'-TGAAAGCGCTTTAT-3', which matches the CRE
consensus sequence proposed by Weickert and Chambliss (41)
except for the last 2 bases. Similar deviations from the CRE consensus
sequence were previously observed in other systems (19).
Sites of hypersensitivity to DNase I digestion were observed when
HPr-Ser-P was present in the reaction mixture, suggesting that binding
of CcpA and HPr-Ser-P might induce changes in the DNA structure. The
protected region contains the sequence 5'-TGAAAGCGCTTTAT-3',
which matches the CRE consensus sequence. The protected sequence
overlaps a 5'-TTGAAA-3' sequence which is the presumed
35
sequence of the acoR promoter. Therefore, we conclude that
repression of transcription of acoR is probably mediated by
the binding of CcpA to the promoter region of acoR. It is
likely that most if not all the catabolite repression of acetoin
utilization by glucose in B. subtilis can be attributed to
the control of transcription of acoR by CcpA.
 |
ACKNOWLEDGMENTS |
We thank Isabelle Martin-Verstraete for helpful discussion, Anne
Galinier for the gift of CcpA, HPr, and HPr-Ser-P, Alex Edelman for
correcting the manuscript, and Christine Dugast for expert secretarial assistance.
This work was supported by research funds from the Institut Pasteur,
the Centre National de la Recherche Scientifique, and the
Ministère de la Recherche. Naima Ould Ali is the recipient of a
grant from the French Ministry of Cooperation and the Algerian Ministry
of Higher Education and Scientific Research.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Unité de
Biochimie Microbienne, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France. Phone: (33) 1 45 68 88 09. Fax: (33) 1 45 68 89 38. E-mail: mdebarbo{at}pasteur.fr.
 |
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Journal of Bacteriology, April 2001, p. 2497-2504, Vol. 183, No. 8
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.8.2497-2504.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
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