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Applied and Environmental Microbiology, December 2006, p. 7723-7729, Vol. 72, No. 12
0099-2240/06/$08.00+0 doi:10.1128/AEM.02002-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Bestowing Inducibility on the Cloned Methanol Dehydrogenase Promoter (PmxaF) of Methylobacterium extorquens by Applying Regulatory Elements of Pseudomonas putida F1
Young J. Choi,1
Lyne Morel,1
Denis Bourque,1
Alaka Mullick,2
Bernard Massie,2 and
Carlos B. Míguez1*
Microbial and Enzymatic Technology Group,1
Genomics & Gene Therapy Vectors Group, Bioprocess Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada2
Received 23 August 2006/
Accepted 4 October 2006

ABSTRACT
P
mxaF is a strong methanol-inducible promoter in
Methylobacterium extorquens. When this promoter is cloned in expression vectors
and used to drive heterologous gene expression, methanol inducibility
is either greatly reduced or entirely lost. In order to bestow
inducibility upon the cloned P
mxaF promoter in expression vectors,
we adopted combinational methods (regulatory elements of the
Pseudomonas putida F1
cym and
cmt operons and Tn
7 transposon
system) to control reporter gene expression at the transcriptional
level in
M. extorquens. An operator fragment (26 nucleotides)
of the
cmt operon was inserted downstream of the cloned P
mxaF promoter in the broad-host-range expression vector (pCHOI3).
The repressor gene (
cymR) located upstream of the
cym operon
in
P. putida F1 was amplified by PCR. To avoid cellular toxicity
for
M. extorquens caused by the overexpression of CymR, single
and/or double copies of
cymR were integrated into the chromosome
of
M. extorquens using the mini-Tn
7 transposon system. Cultures
containing the chromosomally integrated
cymR gene were subsequently
transformed with pCHOI3 containing modified P
mxaF (i.e., P
mxaF plus operator). In this construct, inducibility is afforded
by cumate (
p-isopropylbenzoate). In this report, we describe
the inducible and tightly regulated expression of heterologous
genes (
bgl [for ß-galactosidase],
est [for esterase],
and
gfp [for green fluorescent protein]) in
M. extorquens. This
is the first documented example of an inducible/regulated heterologous
gene expression system in
M. extorquens.

INTRODUCTION
Methylotrophic bacteria are a diverse group of microorganisms
with the ability to utilize single-carbon (C
1) substrates more
reduced than carbon dioxide as their sole source of carbon and
energy. Among the methylotrophs, members of the genus
Methylobacterium have been described as being ubiquitous, participating in a
myriad of favorable interactions with nature (
24,
26,
27). Furthermore,
Methylobacterium spp. naturally produce several substances of
commercial importance, including poly-ß-hydroxybutyrate
(
3,
4), vitamin B
12 (
28), pyrroloquinoline quinone (
1,
10),
and carotenoids (
29). Over the past decade,
Methylobacterium extorquens AM1 has been extensively studied and characterized
both genetically and physiologically (
6,
18,
20). The wealth
and depth of understanding of
M. extorquens and closely related
strains suggest the potential of
M. extorquens as a source of
industrially pertinent natural products and recombinant proteins.
The salient aspects for this potential have been described elsewhere
(
2,
8,
9), and they include (i) simple and inexpensive cultivation
requirements, (ii) optimized high-cell-density fermentation
protocols, (iii) available genome sequence for
M. extorquens AM1, and (iv) availability of suitable genetic tools for
M. extorquens (
8,
13,
19,
21,
22). Application of these tools has
made it possible to overexpress a variety of recombinant proteins
in the range of 3 to 6 g/liter under high-cell-density growth
conditions (
8,
9,
13). However, inducible/regulated expression
of recombinant genes in
M. extorquens or in any other methylotroph,
to our knowledge, has not yet been attained.
M. extorquens possesses
native methanol-inducible promoters, notably promoters which
are located upstream of genes that encode methanol dehydrogenase
and other proteins required for its activity and enzymes required
for the synthesis of the methanol dehydrogenase prosthetic group,
pyrroloquinoline quinone. Of these, the promoter
PmxaF has been
thoroughly scrutinized both biochemically and in expression
studies (
8,
9,
19,
21,
30). In its native form in the chromosome,
this strong promoter is methanol inducible. However, when this
promoter is cloned in expression vectors, it acts essentially
in a constitutive mode. The mechanism by which
PmxaF is regulated
in the chromosome is still not fully known. Therefore, the reason
the recombinant
PmxaF reverts from inducible to constitutive
remains speculative. Expression of the green fluorescent protein
(GFP)-encoding gene (
gfp) under the control of cloned
PmxaF in the plasmid pCM110 was observed even after the culture was
grown repeatedly on succinate as the sole source of carbon (unpublished
results). This fact makes
PmxaF unsuitable in applications where
regulated expression is paramount, such as in expression of
recombinant proteins potentially toxic to the host or in metabolic
flux and pathway engineering applications where the effect of
expression of specific genes on metabolism is required. Several
other heterologous inducible promoters, such as P
lac,

P
L, and
P
R, have been tested with
M. extorquens ATCC 55366; however,
gene expression under the control of these promoters was leaky
and weak (unpublished results). To develop a regulated and inducible
expression system, we adapted the regulatory element of
Pseudomonas putida F1.
P. putida F1 degrades
p-cymene (
p-isopropyltoluene)
through
p-cumate (
p-isopropylbenzoate) to isobutyrate, pyruvate,
and acetyl coenzyme A (
11,
12). The genes encoding the enzymes
required for this degradation are grouped in two distinct operons,
called
cym and
cmt. The
cym operon encodes the conversion of
p-cymene to
p-cumate. Located downstream of the
cym operon is
the
cmt operon, which encodes the catabolism of
p-cumate. A
regulatory protein known as CymR, encoded upstream of the
cym operon, has been shown to bind to specific operator-promoter
regions in both operons and controls expression of both operons.
Induction is afforded by
p-cumate, the end product of the first
operon, but not by
p-cymene (
11,
12).
We decided to apply the regulatory elements, the cymR gene and the operator fragment of the cmt operon from P. putida F1, to M. extorquens ATCC 33566 in the hope of bestowing inducibility and regulation on the existing constitutive expression vectors for Methylobacterium strains. If successful, we would obtain an inducible expression system able to operate during growth of Methylobacterium on a preferred growth substrate, methanol, while controlling the expression of heterologous genes from the strong PmxaF promoter using the nontoxic and inexpensive inducer cumate.

MATERIALS AND METHODS
Bacterial strains and growth conditions.
The bacterial strains and plasmids used in this study are listed
in Table
1.
M. extorquens (ATCC 55366) was used for the preparation
of the heterologous gene expression host.
Escherichia coli strain
Top10 was used for cloning and propagation of recombinant plasmid
DNA, and S17-1
pir (
recA thi pro hsdR M+ RP4:2-Tc:Mu:Km
Tn
7,
pir lysogen; Sm
r Tp
r) was used for propagation of the
helper plasmid (
17).
E. coli was cultured in Luria-Bertani broth
at 37°C.
M. extorquens was grown in CHOI medium, as previously
described (
9), and 1% (vol/vol) methanol was used as the sole
carbon source. Media were solidified by 1.8% agar (Difco) when
appropriate. Antibiotics were used for
E. coli and
M. extorquens at the following concentrations (in µg/ml): ampicillin,
100; kanamycin (Km), 40; tetracycline (Tc), 35.
Construction of expression hosts.
The
M. extorquens expression hosts (CymR1 and CymR2) were constructed
by insertion of the
cymR gene of
P. putida F1 using the mini-Tn
7 integration system with the mini-Tn
7 vector pBRI80 with a helper
plasmid (
12,
17). Primers used in the
cymR amplification were
designed on the basis of the nucleotide sequence of the
P. putida F1
cym operon (
11,
12). In order to achieve tightly regulated
induction, two copies of the
cymR gene were integrated into
the
M. extorquens chromosome. Briefly, the mini-Tn
7 base vector
pBRI80 was constructed as follows: a 1,955-bp PstI fragment
containing
tetA and
tetR was amplified from pCM110 (
19) by PCR
using the primers Tet-F-Pst (5'-G
CTGCAGTCAATCGTCACCCTTTCTCGGTC-3')
(PstI site is underlined) and Tet-R-Pst (5'-G
CTGCAGTCAGCGATCGGCTCGTTGCCCTG-3')
(PstI site is underlined). This fragment was then replaced with
a kanamycin-resistant-protein-encoding gene in pBK-miniTn7-

Sm2
to form pBRI-tet.
The PmxaF promoter plus the ribosomal binding site (PmxaF-RBS) was amplified from pCESTc using the primers MDH-F-Pst (5'-GGCTGCAGGTTGACGACAACGGTGCGATG-3') (PstI site is underlined) and MDH-R-Mlu (5'-CCGACGCGTATGTATATCTCCTTCTTAAAG-3') (MluI site is underlined). The PCR fragment containing PmxaF-RBS was cloned into pBRI-tet, which was partially digested with PstI/MluI to delete the Smr/Spr cassette to generate pBRI80.
To generate pBRI-cymR1, cymR was amplified from chromosomal DNA of P. putida F1 using the primers CYM-F-Afl (5'-GCTTAAGAAGATGGTGATCATGAGTCCAAAGAGAAGAAC3') (AflII site is underlined) and CYM-R-Not (5'-CAGCGGCCGCCTAGCGCTTGAATTTCGCGTACCGCTCTCGCG-3') (NotI site is underlined). A 612-bp AflII-NotI fragment from pCR-cymR was ligated into the AflII-NotI site of pBRI80 to form pBRI-cymR1. To obtain pBRI-cymR2, containing two copies of cymR expression cassettes, a second copy of cymR was amplified from pBRI-cymR using the primers MDH-CYM-F-Not (5'-CAGCGGCCGCGTTGACGACAACGGTGCGATGGGTC-3') (NotI site is underlined) and CYM-R-Apa (5'-CAGGGCCCCTAGCGCTTGAATTTCGCGTACCGCTCTCGCG-3') (ApaI site is underlined). The amplified fragment containing PmxaF-RBS-cymR was then ligated into the NotI-ApaI site of pBRI-cymR1 to generate pBRI-cymR2.
The genotypes of the cymR-integrated host strains were confirmed by Southern hybridization using the 612-bp cymR fragment as a probe. Since we have identified the specific Tn7 insertion site (attTn7) for M. extorquens in a previous study (8), the integration of the target gene into the chromosome of M. extorquens was also determined by colony PCR using designed primers which include common Tn7 primers (PTn7RF, 5'-ATTAGCTTACGACGCTACACCC-3'; PTn7LR, 5'-CACAGCATAACTGGACTGATTTC-3') and gene-specific primers (PdhaTF, 5'-CATCGCGATTGTCGATTCGG-3'; and PglmSR, 5'-CTGAAGGAAATCAGCTACATC-3'). The cymR-positive strains were finally confirmed by Western blotting. Then, the electrocompetent cells were prepared using cymR-positive M. extorquens, essentially as described previously (9, 13).
Inducible expression vector construction.
Manipulations and sequencing of DNA were carried out using standard procedures. The operator sequence of the cmt operon from P. putida F1 was introduced downstream of the methanol dehydrogenase promoter, PmxaF, by PCR. The pCUM50 regulative expression vector was obtained in several steps: first, the PmxaF plus synthetic operator sequence (PmxaF+operator) was amplified by PCR from pCM110 using primers MDH-F-PST (5'-GCTGCAGGTCGACTCTAGATCACCTCCTTAAGC-3') (the PstI site is underlined) and MDH-CUM-R (5'-CGAATTCATAATACAAACAGACCAGATTGTCTGTTTGTTGCCCTTAGGATCCGCGGTATC-3') (the EcoRI site is underlined). The 403-bp PCR fragment containing PmxaF+operator was cloned into pCR2.1 to create pCR-MDHOP. Next, the kanamycin resistance gene of a 1,218-bp PstI fragment from pBK-miniTn7-
Sm2 was cloned into the PstI site of pCM110, and then tetA and tetR were removed by restriction with BclI and self-ligation yielded pCHOI3. A 403-bp PstI-EcoRI fragment from pCR-MDHOP was then ligated between the PstI and EcoRI sites of pCHOI3; this replaced PmxaF with PmxaF+operator to form the cumate-inducible expression vector pCUM50.
To test heterologous protein production using this cumate switch system, we obtained an XbaI-ClaI fragment containing the gfp gene from pQBI63 and cloned it into SpeI-ClaI sites of pCUM50 to generate pCUM-gfp. The 2,100-bp fragment carrying the lactase gene (bgl) from Bifidobacterium infantis was amplified from pEBIG4 (15) using primers BGL-F-Nhe (5'-CGCTAGCGAACATAGAGCGTTCAAGTGGC-3') (the NheI site is underlined) and BGL-R-Cla (5'-CATCGATTTACAGCTTGACGACGAGTACGCCG-3') (the ClaI site is underlined). For the amplification of the esterase gene (1,800 bp; estI) of Lactobacillus casei, pCESTa (9) was used as a template with primers EST-F-Nhe (5'-GGCTAGCGATCAATCTAAAACAAATC-3') (the NheI site is underlined) and EST-R-Cla (5'-CATCGATTTATTTATTTGTAATACCGTCTGC-3') (the ClaI site is underlined). These NheI-ClaI fragments of bgl and est were then replaced with a gfp gene in pCUM-gfp to form pCUM-bgl and pCUM-est, respectively. The different proteins tested in the pCUM system were cloned via SpeI and ClaI (pCUM-gfp) or via NheI and ClaI (pCUM-bgl and pCUM-est).
Detection of gene expression.
Detection of GFP was carried out by fluorescence microscopy, and quantification was done using a microplate spectrofluorometer (SPECTRAFluor Plus; TECAN) under excitation and emission wavelengths of 485 and 508 nm, respectively. The concentration of GFP was calculated based on a linear relationship between concentration and fluorescence units determined using solutions of purified GFP (Qbiogene). The biomass was determined by cell dry weight measurement of the samples (Moisture Analyzer MA 30; Sartorius).
Esterase activity was determined by a spectrophotometric method using para-nitrophenyl caprylate as a substrate. The rate of hydrolysis of para-nitrophenyl caprylate at 37°C was measured in 50 mM sodium phosphate buffer (pH 7.0) according to the method described previously (9, 16). One unit of activity was defined as the amount of enzyme that liberated 1 µmol of p-nitrophenol per min under the given assay conditions. The ß-galactosidase activity was measured with o-nitrophenol-ß-D-galactopyranoside as a substrate, and one unit of activity was defined as the amount of enzyme that liberated 1 µmol of o-nitrophenol per min (25). The protein concentration was estimated by the method of Bradford (5) using the Bio-Rad protein assay kit with bovine serum albumin as a standard.
Western blotting.
Integrative expression of the repressor protein (CymR) was determined by Western blotting using a standard protocol. CymR was detected with rabbit anti-bCymR no. 422 antibody (0.1 g ml1; in-house antibody generated by our group) and a goat anti-rabbit immunoglobulin G (heavy plus light chains) horseradish peroxidase conjugate (0.1 µg ml1; catalog no. 31460; Pierce, West Grove, PA). Cells were lysed in sodium dodecyl sulfate-polyacrylamide gel electrophoresis sample buffer.

RESULTS AND DISCUSSION
The construction of the cumate-regulated/inducible system in
M. extorquens required the engineering both of the chromosome
and of the cloned P
mxaF promoter, described hereafter. The structural
components required for an operational cumate-regulated expression
system are the
cymR gene, which encodes the CymR repressor protein,
and the CymR binding DNA region fused to the 3' end of a selected
promoter. For the cumate-regulated system to work effectively
in
M. extorquens, the culture must be able to express and produce
the functional repressor protein (CymR) constitutively. First,
the 612-bp
cymR gene from
P. putida F1 was cloned into pCM110
under the control of the P
mxaF promoter. CymR expression was
confirmed by Western blot analysis (Fig.
1c). However, the culture
grew very poorly (data not shown), indicating a potential toxicity
of CymR to the host. In order to reduce the level of CymR production
and, by inference, its toxicity, an alternative to the plasmid-based
cymR expression was adopted. In the absence of information on
the minimal amount of CymR required for optimal repression of
transcription, DNA fragments containing either one or two copies
of the
cymR gene were integrated into the chromosome of
M. extorquens,
generating the clones
M. extorquens (CymR1) and
M. extorquens (CymR2), respectively. Integration was achieved using the mini-Tn
7 transposon system described elsewhere (
7,
8). Insertion of mini-Tn
7-P
mxaF-cymR into the unique Tn
7 attachment site (
attTn
7) of
M. extorquens was verified by colony PCR (Fig.
1a). Expression was once again
confirmed by Western blot analysis (Fig.
1b). Importantly, growth
of the
cymR-expressing clones was indistinguishable from that
of wild-type
M. extorquens (data not shown). To verify if the
levels of CymR produced by the transformants were sufficient
to repress transcription and thereby regulate expression, an
expression vector possessing the engineered P
mxaF promoter had
to be constructed. The expression vector (pCUM50) was constructed
containing the operator sequence of the
cmt operon from
P. putida F1 downstream of the cloned homogeneous promoter, P
mxaF, in
pCHOI3, a derivative of pCM110 where the tetracycline marker
was exchanged for kanamycin (Table
1). Three different constructs
containing a gene encoding GFP, esterase, or ß-galactosidase
were inserted into the multiple cloning site downstream of the
operator, generating pCUM-gfp, pCUM-est, or pCUM-bgl, respectively
(Fig.
2). Expression of GFP in the recombinant host
M. extorquens (CymR2) transformed with the expression vector pCUM-gfp was
not detected in the absence of the inducer, cumate. However,
the recombinant host
M. extorquens (CymR1) transformed with
the expression vector pCUM-gfp grown in the absence of the inducer
showed leaky expression, amounting to 15 mg GFP/g dry biomass.
This leaky expression represents about 20% of the GFP yield
of a fully cumate-induced culture (80 mg GFP/g dry biomass).
Incomplete repression in
M. extorquens (CymR1) hosts was assumed
to be due to the insufficient CymR production (Fig.
1c). Hence,
competent cells containing two
cymR copies [
M. extorquens (CymR2)]
were used for further studies.
M. extorquens (CymR2) transformed with the plasmids pCUM-gfp,
pCUM-est, and pCUM-bgl grew well, and expression could not be
detected in the absence of cumate. The addition of cumate to
the culture reduces the binding capacity of the repressor protein
(CymR) for the operator region, and transcriptional repression
is thereby alleviated. Tight inducible expression of the reporter
gene is thereby attained. The basic mechanism of this system
is summarized in Fig.
3. The optimal inducer concentration for
recombinant
M. extorquens (CymR2) transformed with pCUM-gfp
was determined in shake flask cultures grown to the mid-log
phase (0.8 to 1.0 units at an optical density at 600 nm [OD
600])
at 30°C, followed by induction with cumate at different
concentrations, ranging from 1 to 30 µg cumate/ml. GFP
expression was detectable at 4 h postinduction at all concentrations
tested. Cumate induction was shown to be very sensitive, since
the addition of 1 µg cumate/ml resulted in GFP production
representing approximately 47% of the GFP yield of a culture
fully induced with 15 µg cumate/ml (data not shown). Growth
inhibition was not observed with the cumate concentrations tested
(1 to 30 µg/ml), indicating that cumate does not negatively
affect cell metabolism at these concentrations in shake flask
experiments, where typical biomass yields are expected to reach
1.5 to 1.7 g of cells (dry weight)/liter. The optimal cumate
concentration for effective induction of GFP expression in shake
flask growth experiments was 15 µg/ml (approximately 0.1
mM). Understandably, in high-cell-density fermentations, where
biomass yields can reach over 50 g of cells (dry weight) per
liter, higher concentrations of cumate may be required.
To determine the optimal time of induction for maximal protein
production,
M. extorquens (CymR2) cells stably transformed with
pCUM-gfp were induced at different stages of growth (OD
600 of
0.4, 0.6, 0.8, 1.0, and 1.2) in shake flask experiments with
15 µg cumate/ml. Cells induced at an OD
600 of 0.8 to 1.0
generated maximal specific yields of GFP. At these induction
points, the specific yield of the recombinant protein was consistently
20 to 50% greater than at other induction points (Fig.
4). However,
it should be noted that stationary-phase cultures could still
be induced, albeit resulting in reduced levels of expression
(data not shown).
To further validate cumate inducibility, we expressed two other
proteins (esterase and ß-galactosidase) in the recombinant
host strain
M. extorquens (CymR2). These transformants were
analyzed for induction profiles and expression levels and were
compared to GFP-expressing cultures. All clones, cultured up
to an OD
600 of 0.8 to 1.0, did not produce detectable levels
of recombinant proteins in the absence of cumate (Fig.
5). In
all cases, at 4 h postinduction with 15 µg cumate/ml,
expression of the recombinant proteins was detected. Production
of GFP, esterase, and ß-galactosidase remained active
even after 24 h postinduction, with maximum expression at 30
h postinduction (Fig.
5a, b, and c). The recombinant protein
expression was not detected in noninduced cells, and the expression
occurred as long as there was cell growth. Using this system,
6.1 g GFP/liter and 5,637 ± 320 and 6,742 ± 480
U of recombinant esterase and ß-galactosidase were
obtained, respectively (Fig.
5a, b, and c).
The well-characterized promoters (T
5, T
7, and
lac) utilized
in
E. coli expression vectors require isopropyl-ß-
D-thiogalactopyranoside
for induction. Although isopropyl-ß-
D-thiogalactopyranoside
is an effective inducer for
E. coli, it is expensive and can
elicit cellular toxicity at concentrations which are deemed
optimal for expression of recombinant proteins (
14,
23). The
innovative aspect of our inducible system is the fact that we
have kept a powerful native promoter for heterologous gene expression,
added an operator region downstream of the promoter, and integrated
a repressor-encoding sequence in the chromosome which expresses
sufficient repressor protein to repress expression of the target
gene completely. Furthermore, cumate, a nontoxic organic and
nonmetabolizable compound for
M. extorquens, at low concentrations
is capable of traversing the cell's outer membranes and alleviates
repression effectively. Cumate did not cause any growth inhibition
even at concentrations twofold higher than that required for
optimal induction. This is the first documented description
of a tightly regulated recombinant expression system in
M. extorquens.
Temporal expression of selected gene products and applications
in metabolic flux and pathway engineering may now be possible
with
M. extorquens.

ACKNOWLEDGMENTS
We gratefully acknowledge A. R. Theisen and M. Pacheco-Oliver
for helpful comments and critical review of the manuscript.

FOOTNOTES
* Corresponding author. Mailing address: Microbial and Enzymatic Technology Group, Bioprocess Sector, Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave., Montreal, Quebec H4P 2R2, Canada. Phone: (514) 496-6280. Fax: (514) 496-7251. E-mail:
carlos.miguez{at}nrc-cnrc.gc.ca.

Published ahead of print on 13 October 2006. 

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Applied and Environmental Microbiology, December 2006, p. 7723-7729, Vol. 72, No. 12
0099-2240/06/$08.00+0 doi:10.1128/AEM.02002-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.