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Applied and Environmental Microbiology, July 2006, p. 5126-5131, Vol. 72, No. 7
0099-2240/06/$08.00+0 doi:10.1128/AEM.00437-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
A Functional mobA Gene for Molybdopterin Cytosine Dinucleotide Cofactor Biosynthesis Is Required for Activity and Holoenzyme Assembly of the Heterotrimeric Nicotine Dehydrogenases of Arthrobacter nicotinovorans
Paula Sachelaru,1
Emile Schiltz,2 and
Roderich Brandsch1*
Institute of Biochemistry and Molecular Biology,1
Institute of Organic Chemistry and Biochemistry, University of Freiburg, Freiburg, Germany2
Received 23 February 2006/
Accepted 4 May 2006

ABSTRACT
Two
Arthrobacter nicotinovorans molybdenum enzymes hydroxylate
the pyridine ring of nicotine. Molybdopterin cytosine dinucleotide
(MCD) was determined to be a cofactor of these enzymes. A
mobA gene responsible for the formation of MCD could be identified
and its function shown to be required for assembly of the heterotrimeric
molybdenum enzymes.

INTRODUCTION
The highly toxic alkaloid nicotine present in tobacco waste
is removed from the environment by mineralization through soil
bacteria. The best-characterized pathway of nicotine degradation
is the one encoded by the megaplasmid pAO1 of
Arthrobacter nicotinovorans (
15). It includes two hydroxylations of the pyridine ring of
nicotine, at C-6 and C-2, and an oxidation at C-2' of the pyrrolidine
ring, which prepare the molecule for its degradation (
4). The
enzymes which perform the hydroxylation reactions belong to
a group of related heterotrimeric bacterial molybdenum oxidoreductases
(
14) composed of a middle-sized subunit (about 30 kDa) carrying
a flavin adenine dinucleotide (FAD) molecule, a small subunit
(about 17 kDa) with two [2Fe-2S] clusters, and a large subunit
(about 85 kDa) carrying a molybdenum cofactor (
19). Nicotine
dehydrogenase (NDH; also called nicotine:acceptor oxidoreductase,
hydroxylating) of
A. nicotinovorans has been characterized before
(
9). The genes of its subunits form an operon (
12,
15). The
genes of a second, related enzyme which is active at pyridine
C-2, 6-hydroxy-pseudooxynicotine:acceptor oxidoreductase, hydroxylating
(known as "ketone" dehydrogenase [KDH]), showed an unexpected
arrangement and were proposed to be carried by a discontinuous
gene cluster (
1). The large molybdenum-containing subunit (KdhL)
gene was tentatively located on pAO1 more than 4,000 bp apart
and transcribed divergently from the genes of the middle (KdhM)
and small (KdhS) subunits (
15). Functional proof of the identity
of the KDH subunit genes was missing.
In bacteria, the molybdenum cofactor may take the form of a molybdenum dinucleotide produced by the addition of a nucleoside monophosphate to molybdopterin, a reaction catalyzed by the MobA protein. In Escherichia coli, the cofactor is a molybdopterin guanosine dinucleotide, and the GTP:molybdopterin guanylyl transferase MobA was studied recently in great detail (13). Other bacteria make use of a molybdopterin cytosine dinucleotide (MCD) cofactor (3, 8, 11). A mobA gene encoding the MobA protein with cytidylyl transferase activity has not yet been described. The nature of the molybdenum cofactor of the nicotine hydroxylating enzymes was not known.
Here we demonstrate the identity of the kdh genes by the assembly of the functional holoenzyme from its three subunits and show that the molybdenum cofactor is MCD. We identify the mobA gene required for the synthesis of MCD and show that the assembly of the KDH and NDH subunits depends on a functional mobA gene and thus on the dinucleotide form of the molybdenum cofactor.

Expression of kdhL and ndhL genes from pART2 transformed into A. nicotinovorans.
The
E. coli-Arthrobacter shuttle vector pART2 allows nicotine-induced
expression of cloned genes in
Arthrobacter species from the
6hdno promoter (
21) in such a way that the synthesized proteins
exhibit a C-terminal His
8 tag. The
kdhL gene was amplified from
A. nicotinovorans whole cells by PCR with the primer pair listed
in Table
1, digested with DraI and XbaI, and inserted by ligation
into the multiple cloning sites of pART2.
E. coli XL-1 Blue
transformed with the ligated DNA was selected on Luria-Bertani
(LB) plates with 50 µg/ml kanamycin. Clones carrying pART2
kdhL recombinant DNA were identified by restriction endonuclease
digestion of plasmid DNAs isolated from individual colonies.
Cloning of
kdhL into this vector resulted, besides the His tag,
in an N-terminal MDPTSSTL
M amino acid sequence extension of
recombinant KdhL (the underlined "M" represents the start methionine
of native KdhL). Recombinant KdhL was isolated by Ni-chelating
chromatography from extracts of pART2
kdhL-transformed
A. nicotinovorans grown at 30°C on citrate medium supplemented with vitamins,
trace elements, and 3 mM
L-nicotine (
5), as described previously
(
6). Analysis of the proteins eluted from the column revealed
that besides the large subunit of the enzyme, the native middle
and small subunits were coeluted (Fig.
1A), in agreement with
the KDH activity of the eluted protein (not shown). When
ndhL,
amplified by PCR with the primer pair indicated in Table
1,
was introduced on pART2 into
A. nicotinovorans, all three subunits
of enzymatically active NDH were recovered by Ni-chelating chromatography,
similar to what was found with
kdhL (not shown). For unknown
reasons, the yield of recombinant NDH was only 0.25 mg/liter,
compared to 2.1 mg/liter for recombinant KDH.

Characterization of the nucleotide moiety of the molybdenum cofactor of KDH.
The molybdenum contents of two independent KDH preparations
were first determined in triplicate in a Perkin-Elmer 4110 ZL
atomic absorption spectrometer. A content of 0.80 mol molybdenum
per mol of enzyme was found, which is close to the 0.87 mol
molybdenum per mol of enzyme reported for NDH (
9) and is an
indication that KDH was loaded with the molybdenum cofactor.
Next, KDH was incubated at 95°C for 10 min in the presence
of sulfuric acid (3% [by volume]), which leads to the release
of the nucleotide from the molybdenum dinucleotide cofactor
and of AMP from FAD, the cofactor associated with KdhM (
18).
Following centrifugation, the supernatant was analyzed by high-performance
liquid chromatography (HPLC) on a reversed-phase column (5 µm
by 250 mm by 4.6 mm) (Aqua; Phenomenex, Aschaffenburg, Germany)
and eluted isocratically at room temperature with 0.1% trifluoroacetic
acid in water at a flow rate of 0.75 ml/min. A rapid scanning
detector was used (model 206PHD; Linear Instruments Corp., Sykam,
Gilching, Germany) for detection and spectrum collection. Besides
AMP, the analysis revealed the presence of CMP but not of GMP
(Fig.
1). The small peak present as a shoulder of the AMP peak
had a slightly different elution time from that of GMP and did
not show the typical purine absorption spectrum. When FAD was
treated as described above and analyzed by HPLC, only an AMP
peak was revealed (not shown). The identification of CMP in
the extract indicated that KDH belongs to the MCD-dependent
enzymes. When the same analysis was performed with His-tagged
KdhL isolated from a
mobA-deficient strain (see below), no nucleotide
was detected.

Identification of transcripts of the kdhL-mobA gene cluster in wild-type and ORF310-disrupted strains by reverse transcription-PCR (RT-PCR).
The three subunit genes of
ndh are arranged in the order M-S-L
(Fig.
2A) and form a transcriptional unit (
12). The
kdh genes
are discontinuous and separated by 4.3 kb (Fig.
2A). The assumed
kdhL gene is the first of a gene cluster. It is followed by
the ORF106 and ORF310 genes, with unknown functions, by the
gene for 2,6-dihydroxypyridine hydroxylase, and by the ORF235,
ORF294, ORF297, and ORF363 genes, with unknown functions. The
last two genes of this cluster are a gene similar to
xdhC (
17)
and one similar to
mobA (Fig.
2B). The ORF310 gene was disrupted
with a chloramphenicol resistance cassette (
cmx) (
10) by homologous
recombination. To this end,
cmx was inserted into the PmlI site
of the ORF310 gene carried on pH6EX3 (
2), which is unable to
replicate in
A. nicotinovorans. The pH6EX3 construct carrying
the
cmx-disrupted ORF310 gene was transformed into
A. nicotinovorans by electroporation and selected on chloramphenicol (22 µg/ml)
plates, and colonies carrying a disrupted ORF310 gene were identified
by PCR (
7). Attempts to disrupt the genes similar to
xdhC and
mobA were unsuccessful.
RT-PCR was performed with nicotine-grown
A. nicotinovorans bacteria
as described previously (
6,
20), using primer pairs derived
from the end of one gene and from the start of the next gene
(Table
1). The genes from
kdhL to the ORF294 gene were apparently
transcribed into one RNA, and those from the ORF297 gene to
mobA were transcribed into a second RNA molecule (Fig.
2B),
since no amplification product was obtained between the ORF294
and ORF297 genes (Fig.
2B, lanes X). The same analysis performed
with RNA prepared from the ORF310-disrupted strain revealed
that transcripts of genes downstream of the inserted chloramphenicol
resistance cassette were no longer detectable, including those
from the ORF297 gene to
mobA (Fig.
2C). Transcripts of
kdhL as well as
kdhMS were present (Fig.
2D). These results suggest
that insertion of
cmx into the ORF310 gene leads to the inactivation
of downstream genes, including those similar to
xdhC and
mobA.
No transcripts of these genes could be detected in A. nicotinovorans bacteria grown in the absence of nicotine (not shown).

NDH and KDH enzyme activities in the cmx-disrupted strain and complementation of the strain with the pAO1 genes similar to xdhC and mobA.
In the
cmx-disrupted strain, no NDH or KDH activity could be
measured. Transcripts of the
kdhL and
kdhMS genes (Fig.
2D)
or
ndh genes (not shown), however, were present. Since no transcripts
of the genes similar to
xdhC and
mobA were seen in the disrupted
strain but the XdhC and MobA proteins were implicated in molybdenum
cofactor insertion into xanthine dehydrogenase (
16,
17) and
molybdopterin dinucleotide biosynthesis (
13), respectively,
we introduced these genes into the ORF310-disrupted strain.
The catabolism of nicotine requires active NDH and KDH, and
its end product, nicotine blue, is an indicator that the pathway
is active. The wild-type strain produced blue pigment on nicotine
plates, but the disrupted strain, which showed no NDH or KDH
activity, did not (Fig.
3, wt and ORF310::
cmx).
Both
xdhC and
mobA or
xdhC and
mobA individually were amplified
from
A. nicotinovorans whole cells in PCRs with the primer pairs
listed in Table
1, and the restriction enzyme-digested PCR products
were inserted into the multiple cloning site of pART2 (
21).
When the genes similar to
xdhC and
mobA were introduced on pART2
into the disrupted strain, the transformants regained the ability
to produce blue pigment on nicotine plates (Fig.
3A, ORF310:
cmx/pART2
xdhCmobA).
Complementation with the gene similar to
mobA only proved sufficient
to restore blue pigment formation (Fig.
3A, ORF310::
cmx/pART2
mobA).
The
cmx-disrupted strain complemented with pART2
xdhC only did
not produce blue pigment (not shown) and looked identical to
the plate shown for the
cmx-disrupted strain without complementation.
The function of the gene similar to
xdhC in
A. nicotinovorans remains to be established.

Recovery of holoenzyme containing His-tagged KdhL from cmx-disrupted ORF310 strain and mobA-complemented A. nicotinovorans.
A. nicotinovorans with
cmx-disrupted ORF310 was transformed
with pART2
kdhL. When a bacterial extract was prepared from this
strain and passed over Ni-chelating Sepharose, only recombinant
KdhL was recovered (Fig.
3B). However, when the strain was transformed
with pART2 carrying
mobA in addition to
kdhL (pART2
mobAkdhL),
all three subunits of KDH were isolated, and the holoenzyme
showed the same specific activity as the holoenzyme assembled
in the wild-type strain transformed with pART2
kdhL (Fig.
3B).
The same result was obtained when an extract of pART2
ndhL-transformed
bacteria was used (not shown).
A scattered arrangement of the subunit genes of an enzyme is unusual. It requires the correlated biosynthesis and stoichiometric assembly of subunits produced from genes transcribed from different promoters. Therefore, experimental proof was required for the assignment of the kdh genes (1). This was provided by the assembly of the recombinant KdhL subunit with the native KdhM and KdhS subunits into the active KDH holoenzyme.
KDH was shown here to be an enzyme with an MCD cofactor. The MobA variant responsible for its synthesis was unknown. Our results strongly suggest that the pAO1 mobA-like gene encodes this molybdenum cofactor cytidylyl transferase. Despite many attempts, our efforts to isolate MobA in soluble form failed. Therefore, we could not test its enzyme specificity in vitro. However, the mobA complementation studies support the functional assignment of MobA as a molybdopterin cytosine dinucleotide biosynthesis protein. The low yield of NDH holoenzyme prevented formal proof of the nature of its cofactor. Since the lack of mobA expression abolished the enzyme activity of KDH as well as NDH, we consider it a reasonable assumption that NDH also contains a molybdopterin cytosine dinucleotide.
Our results show that the synthesis of MCD, and thus that of a functional MCD biosynthesis protein, MobA, is required for the assembly of the heterotrimeric KDH holoenzyme. Inability to synthesize the dinucleotide form of the molybdenum cofactor because of a deficient mobA gene resulted in the failure to assemble the holoenzyme.

ACKNOWLEDGMENTS
This work was supported by a grant of the Deutsche Forschungsgemeinschaft
to R.B.

FOOTNOTES
* Corresponding author. Mailing address: Institute for Biochemistry and Molecular Biology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg, Germany. Phone: 49-761-2035231. Fax: 49-761-2035253. E-mail:
roderich.brandsch{at}biochemie.uni-freiburg.de.


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Applied and Environmental Microbiology, July 2006, p. 5126-5131, Vol. 72, No. 7
0099-2240/06/$08.00+0 doi:10.1128/AEM.00437-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
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