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Journal of Bacteriology, June 1999, p. 3837-3841, Vol. 181, No. 12
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
Biochemical and Molecular Characterization of the
Bacillus subtilis Acetoin Catabolic Pathway
Min
Huang,
Fred Bernd
Oppermann-Sanio, and
Alexander
Steinbüchel*
Institut für Mikrobiologie der
Westfälischen Wilhelms-Universität Münster, D-48149
Münster, Germany
Received 2 October 1998/Accepted 5 April 1999
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ABSTRACT |
A recent study indicated that Bacillus subtilis
catabolizes acetoin by enzymes encoded by the acu gene
cluster (F. J. Grundy, D. A. Waters, T. Y. Takova, and
T. M. Henkin, Mol. Microbiol. 10:259-271, 1993) that are
completely different from those in the multicomponent acetoin
dehydrogenase enzyme system (AoDH ES) encoded by aco gene
clusters found before in all other bacteria capable of utilizing
acetoin as the sole carbon source for growth. By hybridization with a
DNA probe covering acoA and acoB of the AoDH ES
from Clostridium magnum, genomic fragments from B. subtilis harboring acoA, acoB,
acoC, acoL, and acoR homologous
genes were identified, and some of them were functionally expressed in
E. coli. Furthermore, acoA was inactivated in
B. subtilis by disruptive mutagenesis; these mutants were
impaired to express PPi-dependent AoDH E1 activity to
remove acetoin from the medium and to grow with acetoin as the carbon
source. Therefore, acetoin is catabolized in B. subtilis by
the same mechanism as all other bacteria investigated so far, leaving
the function of the previously described acu genes obscure.
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TEXT |
Acetoin is a product of fermentative
metabolism in many prokaryotic and eukaryotic microorganisms and also
in Bacillus spp. (20). For 70 years it has been
known that bacteria are capable of using acetoin as their sole carbon
source for growth (33). Detailed knowledge about the
catabolism of acetoin was obtained from studies on a diversity of
acetoin-utilizing bacteria, such as Pelobacter carbinolicus
(21, 22), Clostridium magnum (16), Klebsiella pneumoniae (6), Alcaligenes
eutrophus (23), and Pseudomonas putida
(15). In those bacteria, acetoin breakdown is catalyzed by
the acetoin dehydrogenase enzyme system (AoDH ES), which consists of
thiamine PPi-dependent acetoin dehydrogenase (AoDH E1),
dihydrolipoamide acetyltransferase (AoDH E2), and dihydrolipoamide dehydrogenase (AoDH E3) (21, 22). The structural genes of the AoDH ES acoA (encoding the
subunit of AoDH E1),
acoB (encoding the
subunit of AoDH E1), and
acoC (encoding AoDH E2) were found to be clustered in a
colinear orientation in the genomes of the bacteria mentioned above
(6, 15, 16, 22, 23). In P. carbinolicus, C. magnum, and K. pneumoniae acoL genes (encoding AoDH E3)
are also part of the aco gene clusters.
The genes encoding the enzymes for acetoin formation form a single
operon in Bacillus subtilis (24), and acetoin
acts as an external carbon storage material that is synthesized and
excreted during exponential growth. B. subtilis also
utilizes acetoin by a yet-unknown pathway during the stationary growth
phase, serving as a carbon and energy source during sporulation
(19). In B. subtilis a gene cluster,
acuABC, was recently identified. The disruption of
acuA diminished the ability to utilize acetoin (10, 11). The acu genes are regulated by the adjacent
ccpA, a trans-acting gene (10). The
acuABC-encoded putative products do not exhibit any
similarity to the aco-encoded components of the AoDH ESs
mentioned above. Because of some structural similarity to the
Escherichia coli ato operon, which encodes proteins involved
in acetoacetate metabolism, the acuABC cluster of B. subtilis was instead supposed to encode proteins that catalyze the
breakdown of acetoin or an unknown derivative by a similar mode as the
ato-encoded system does, i.e., by coenzyme A transfer and
subsequent cleavage (11). The unexpected designation of the
recently described acu genes to acetoin catabolism in
B. subtilis lacking homologies to the well-characterized
aco genes prompted us to reinvestigate the catabolism of
acetoin in B. subtilis. Understanding the catabolism of
acetoin in B. subtilis will also be interesting from a
historical perspective, since early studies on this subject resulted in
the wrong hypothesis that acetoin is degraded via the 2,3-butanediol cycle which was also mentioned in some text books (e.g., reference 8).
In order to investigate if B. subtilis 168 (DSMZ 402)
possesses genes homologous to the known aco genes encoding
the components involved in the AoDH ES, totally
PstI-digested genomic DNA was screened by Southern
hybridization (15) with a 1.6-kbp EcoRI fragment
from C. magnum (16) containing the most conserved
region of acoA and acoB and having a similar G+C
content (22). This DNA probe gave a clear single signal,
which corresponded to a 4.2-kbp PstI fragment. Restriction
fragments of the corresponding size were separated electrophoretically
and were isolated from the agarose gel by the filter technique
(31). The fragments were subsequently ligated with
PstI-restricted pBluescript SK(
) (Stratagene Cloning
Systems, San Diego, Calif.) and transformed into E. coli
DH5
(9) by the calcium chloride procedure
(25). Colony hybridization (12) identified clones
harboring a 4.2-kbp PstI fragment, which was referred to as
P42 (Fig. 1). By employing subfragments
of P42, a 3.4-kbp EcoRI fragment (referred to as E34) (Fig.
1) and a 2.8-kbp BamHI fragment (referred to as B28) (Fig.
1) were also identified. The nucleotide sequences of a region of 7,343 bp was obtained from both strands of P42, E34, and B28 (26);
analysis of the nucleotide sequences, which was performed with the
programs from the Heidelberg Unix Sequence Analysis Resources (release
4.0), revealed five major open reading frames (ORFs), which were
designated acoA, acoB, acoC,
acoL, and acoR (Fig. 1), capable of encoding
polypeptides with molecular weights of 36,030, 36,821, 42,798, 48,822, and 64,938, respectively. The intergenic regions between
acoA and acoB, acoB and
acoC, acoC and acoL, and acoL and acoR comprised only 3, 13, 28, or 115 bp, respectively. In addition, ORF1 was identified 232 bp upstream from
acoA. The obtained sequence was totally different from that
of the acu gene cluster (10, 11). It was
identical with the sequence recently deposited in the data bank by
others (17, 34), except for a few minor deviations in the
carboxy-terminal region of acoC and one deviation in
acoR, which all occurred in not highly conserved regions.
The sequence obtained in this study was submitted to the National
Center for Biotechnology Information on 30 May 1997 under accession no.
AF006075.

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FIG. 1.
Molecular organization of the B. subtilis aco
gene cluster. (A) Scale in kilobase pairs. (B) Structural genes of the
aco gene cluster. The positions of putative promoters (P)
and hairpin-like structures (loops) are indicated. (C) Relevant
restriction sites of the sequenced region. (D) Relevant fragments of
the analyzed region.
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The deduced amino acid sequences of the identified ORFs were compared
to data files in the SWISSPROT and EMBL data libraries in a homology
search. Striking similarities between the acoABCL-encoded amino acid sequences and the corresponding enzyme components of the
well-known AoDH ES from P. putida (15), P. carbinolicus (22), A. eutrophus
(23), C. magnum (16), and K. pneumoniae (6) were found.
As in other thiamine PPi-dependent enzymes, a putative
thiamine PPi-binding region (13) and other
characteristic motifs (32) were identified in the central
region of the deduced amino acid sequence of AcoA. The N-terminal
region of B. subtilis AcoC shares most characteristics with
the dihydrolipoamide acyltransferases of various origins
such as
Lys43, which is presumably lipoylated, and
Gly33 and Gly54, which flank this lysine
residue
and with the corresponding C-terminal catalytic domains of
various dihydrolipoamide acyltransferases, including the conserved
putative active-site histidine-aspartate couple (3, 16, 22).
AcoL exhibited the putative flavin adenine dinucleotide-binding domain
(5) at the N-terminal region, an active disulfide bridge
site at position Cys38 and Cys43, a putative
NAD(H)-binding region in the central part, and the putative interface
region at the C terminus and therefore matched the characteristic
properties of dihydrolipoamide dehydrogenases (16, 22).
Comparative sequence alignments of the putative acoR
translational product revealed striking similarities to the conserved C
domains of various
24/
12 promoter activating proteins, which are
involved in the interaction with
54-dependent RNA
polymerases (29). ORF1 putatively encodes a
195-amino-residue polypeptide upstream from acoA (Fig. 1)
that exhibits weak homologies to the DNA helicase-like protein or
ribosomal protein L6.
A sequence that well matched the enterobacterial
54
consensus sequence (30) and other specific upstream
activator sequences of the aco gene clusters from A. eutrophus, C. magnum, and P. putida
(15, 16, 23) was localized 39 bp upstream of
acoA. In addition, 66 bp upstream of acoR a
sequence exhibiting strong homology to the B. subtilis
43 promoter consensus sequence (7) as well as
to the E. coli
70 (
35/
10) promoter
sequence (14) was found. A second
24/
12-like promoter
sequence was found 31 bp preceding the start codon of acoL.
Inverted repeats were identified 6 bp downstream from acoL and 100 bp upstream from acoA, thus further indicating the
separation of acoR and ORF1 from the genes of a putative
acoABCL operon.
To investigate the physiological function of the aco genes
for the acetoin catabolism in B. subtilis, the expression of
intact AoDH ES was switched off by disruptive mutagenesis. For this
purpose the integrational plasmid pLGSA700 was constructed (Fig.
2). This plasmid encoded part of the
subunit of AoDH E1, which is the key component of the AoDH ES (16,
22), and was used to disrupt the first gene of the aco
cluster. After transforming B. subtilis 168, which was done
as described previously (2), chloramphenicol-resistant strains were obtained; these were referred to as SA35, SA36, SA37, SA41, SA42, and SA43, respectively. The integration of pLGSA700 into
B. subtilis 168 acoA through Campbell-type
recombination (4) was confirmed by Southern hybridization
(22, 25) of PstI- and EcoRI-digested
genomic DNA with vector DNA (pLGW200) as a probe (Fig.
3). Whereas no signal was obtained in the
DNA of the wild type, bands were detected in the DNAs of the
acoA-defective mutants corresponding to PstI
fragments of 8.4 kbp and to EcoRI fragments of 10.5 kbp,
respectively. No signals corresponding to the size of pLGSA700 (7.5 kbp) were obtained. This result is in accordance with the integration
of pLGSA700 by single crossover events into the SA700-homologous
region of the acoA-defective mutants, which is located 1.1 kbp downstream of a PstI-site (Fig. 2) and 3.3 kbp
downstream of an EcoRI-site (17).

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FIG. 2.
Disruptive mutagenesis of acoA. By PCR a
700-bp DNA fragment of acoA, covering the inner region of
acoA, was synthesized, and this fragment was inserted into
pLGW200 (1). The ligation mixture was transformed into
E. coli Top10 (Invitrogen, San Diego, Calif.) for
amplification. The isolated recombinant plasmid pLGSA700 was
transformed into cells of B. subtilis 168, which were
selected for chloramphenicol resistance.
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FIG. 3.
Localization of pLGSA700 integrations. PstI
and EcoRI digests of genomic DNA from B. subtilis
168 (wt) and from pLGSA700-disrupted acoA mutants (SA35,
SA36, SA37, SA41, SA42, and SA43) were separated in 0.8% (wt/vol)
agarose gels, blotted onto a nylon membrane, and hybridized with
biotin-labeled vector pLGW200 (22). The positions of
PstI and EcoRI fragments which gave signals with
the probe are indicated by arrows. The sizes of standard fragments
(Std) are indicated at the left. (A) Agarose gel stained with ethidium
bromide; (B) blot hybridized with probe pLGW200.
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We investigated the growth of the strains in various solidified media.
Cells were plated on solid TSS medium, which was supplemented with
0.01% (wt/vol) sodium glutamate (11). As main C sources, 0.2% (wt/vol) acetoin or 0.2% (wt/vol) glucose (positive control) was
added. The following B. subtilis strains were tested: (i) 168 (wild type), (ii) an acoA mutant of 168 (SA35), and
(iii) SMY (wild type); the third strain is the same one used by Grundy et al. (11). All three strains showed the same growth
behavior: whereas good growth was obtained with glucose (positive
control) after 1 day, only very weak growth was obtained both in the
presence and absence of acetoin (negative control) even after 1 week of incubation. These results are not surprising, because acetoin (like
2,3-butanediol) is used by B. subtilis only during the
stationary phase, when it serves as a C source for sporulation.
Therefore, the degradation of acetoin is usually investigated with
stationary cells (19).
Growth was also investigated in liquid culture. Acetoin was added to
stationary cells of B. subtilis 168 and acoA
mutant SA35, which were grown in NSM medium (27), and the
culture supernatant was monitored by gas chromatography as described
before (28). As seen in Fig.
4, the mutant SA35 was unable to utilize
acetoin as a carbon source, while the wild type started growing and
kept doing so after the addition of acetoin. Regarding growth, the mutant behaved similar to the wild type without added acetoin. In
accordance with this, AoDH E1 was present in extracts of stationary wild-type cells (0.016 U/mg of protein), while cell extracts of SA35
contained no detectable activity (<0.003 U/mg of protein) and gave no
stained band in the protein pattern during activity staining. The
mutation did not effect the cells' ability to synthesize acetoin,
which is obvious from the continuous, slight increase of the acetoin
concentration in the medium, even after the addition of acetoin.

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FIG. 4.
Acetoin utilization by B. subtilis 168 and
the acoA-defective mutant SA35. Cells of B. subtilis 168 and of SA35 were cultivated in NSM at 37°C. At the
time point indicated by an arrow, 10 mM acetoin was added to the
culture of SA35 ( , ) and to one culture of B. subtilis
168 ( , ), whereas it was omitted from the other culture of
B. subtilis 168 ( , ). Growth ( , , ) was
monitored photometrically, and acetoin in the culture supernatants
( , , ) was measured gas chromatographically.
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These experiments clearly demonstrated that an aco-encoded
AoDH ES is present in B. subtilis and that it is the major
enzyme system responsible for the catabolism of acetoin. From this and the striking similarities of the aco-encoded proteins of
B. subtilis to the components of AoDH ESs in other bacteria,
we conclude that B. subtilis possesses an enzyme system for
the degradation of acetoin that is similar to the enzyme systems also
responsible for the degradation of acetoin in all other
phylogenetically and physiologically not related bacteria (6, 15,
16, 21-23). The function of the previously described
acu genes (10, 11), the translational products of
which have nothing in common with those in the well-investigated AoDH
ES, remains unclear. It is very likely that these acu genes
interfere with the acetoin catabolism in a nondirect way. To reveal the
function of the acu genes, it will be necessary to assign an
enzyme function to them. Recently, it was found that the
acuC translational product exhibited significant sequence
similarity to different eukaryotic histone deacetylases (18); it seems worthwhile to investigate whether AcuC has a regulatory function like these eucaryotic proteins.
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ACKNOWLEDGMENTS |
The provision of plasmid pLGW200 by J. M. van Dijl and H. Tjalsma is gratefully acknowledged.
This study was supported by a grant from the Deutsche
Forschungsgemeinschaft (Ste 386/3-4) and by a fellowship of the
Deutsche Forschungsanstalt für Luft- und Raumfahrt e. V. to Min Huang.
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FOOTNOTES |
*
Corresponding author. Mailing address: Institut
für Mikrobiologie der Westfälischen
Wilhelms-Universität Münster, Corrensstraße 3, Germany.
Phone: 49-251-8339821. Fax: 49-251-8338388. E-mail: steinbu{at}uni-muenster.de.
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Journal of Bacteriology, June 1999, p. 3837-3841, Vol. 181, No. 12
0021-9193/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.
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