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Antimicrobial Agents and Chemotherapy, January 2004, p. 209-215, Vol. 48, No. 1
0066-4804/04/$08.00+0 DOI: 10.1128/AAC.48.1.209-215.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Constitutive Expression of a Chromosomal Class A (BJM Group 2) ß-Lactamase in Xanthomonas campestris
Shu-Fen Weng,1 Juey-Wen Lin,2 Chih-Hung Chen,1 Yih-Yuan Chen,1 Yi-Hsuan Tseng,1 and Yi-Hsiung Tseng1*
Institute of Molecular Biology,1
Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan, Republic of China2
Received 28 February 2003/
Returned for modification 29 April 2003/
Accepted 23 September 2003

ABSTRACT
Sequencing of the upstream region of the ß-lactamase
gene from
Xanthomonas campestris pv. campestris 11 (
blaXCC-1)
revealed the cognate
ampR1 gene (289 amino acids, 31 kDa). It
runs divergently from
blaXCC-1 with a 100-bp intergenic region
(IG) containing partially overlapped promoters with structural
features typical of the
bla-
ampR IG. The deduced AmpR1 protein
shows significant identity in amino acid sequence and conserved
motifs with AmpR proteins of other species, e.g., of
Pseudomonas aeruginosa (58.2% amino acid identity). Results of insertional
mutation, complementation tests, and ß-lactamase assays
suggested that expression of
blaXCC-1 was constitutive and dependent
on AmpR1. Four
bla genes and two
ampR genes are present in the
fully sequenced
X. campestris pv. campestris ATCC 33913 genome,
with XCC3039 and XCC3040 considered the analogues of
blaXCC-1 and
ampR1, respectively. An
ampR1 homologue was detected by
Southern hybridization in the ampicillin-resistant
Xanthomonas strains, which appear to express ß-lactamase constitutively.
Although the significance remains to be studied, constitutive
expression of ß-lactamase by a widespread bacterial
genus raises environmental concerns regarding the dissemination
of resistance genes.

INTRODUCTION
Xanthomonas campestris pv. campestris is a gram-negative phytopathogenic
bacterium causing black rot in crucifers (
32). In our previous
study, it was found that strains of
Xanthomonas isolated in
Taiwan are commonly resistant to ampicillin at a level of 50
µg/ml (
29). To characterize the resistance property, a
bla gene (renamed
blaXCC-1 in this study) coding for a periplasmic
ß-lactamase of 30 kDa in
X. campestris pv. campestris
11 (strain Xc11) was cloned and sequenced (
6,
29). Its deduced
amino acid sequence shows identity (51.5%) and conserved domains
to the
Stenotrophomonas maltophilia L2 and the other Ambler
class A or Bush group 2 ß-lactamases. Southern hybridization
using the
blaXCC-1-specific probe showed that homologous ß-lactamase
genes were widespread in xanthomonads. In addition, sequencing
data have also revealed the N-terminal 41 codons of the regulatory
ampR gene (designated
ampR1) in the upstream region of
blaXCC-1 (
29).
The expression of ß-lactamase genes (ampC) in members of the family Enterobacteriaceae is under the control of three genes, ampR, ampD, and ampG (3, 10, 12, 19, 23). The ampR gene is usually located immediately upstream of the cognate ß-lactamase gene (ampC) and transcribed divergently, encoding a trans-acting protein (AmpR) which belongs to the LysR family of bacterial regulators (26). In Citrobacter freundii, AmpR has been shown to bind to a 38-bp sequence within the intergenic region (IG) between ampR and ampC (16). It was suggested that in the inactive state, AmpR acts as a weak repressor of ampR transcription, causing a negative autoregulation as in many similar regulatory loci, whereas in the activated state, it acts as a strong activator for the transcription of ampC. AmpG (a permease) and AmpD (a cytosolic amidase) are enzymes involved in cell wall metabolism, required for the transport of murein breakdown products (muropeptides) into the cytoplasm (12). AmpD negatively regulates ampC expression, while AmpG is required for activation of ampC by AmpR. In the chromosomal ampR-ampC systems characterized, the ampC genes are usually inducible (1, 2, 17, 21). The enhanced expression of ampC in Enterobacter, Citrobacter, and Pseudomonas strains with both hyperinducible and high-level constitutive ß-lactamase production has been shown to be due to a mutation in ampD (5, 13).
In this study, we cloned and sequenced the DNA region upstream of the blaXCC-1 gene, revealing the entire ampR1 gene, and tested the effects of mutation in ampR1 on the expression of the blaXCC-1 gene. The results showed that the blaXCC-1 gene appears to be expressed constitutively, requiring the function of AmpR1. All other ampicillin-resistant Xanthomonas strains tested also appear to express ß-lactamase constitutively.

MATERIALS AND METHODS
Bacterial strains and growth conditions.
The strains used in this study are listed in Table
1. Luria-Bertani
(LB) medium and L agar (
18) were used as the general-purpose
media for cultivation of
Xanthomonas (28°C),
Serratia (37°C),
and
Escherichia coli (37°C). Antibiotics were added when
necessary: ampicillin (50 µg/ml), kanamycin (50 µg/ml),
and tetracycline (15 µg/ml).
Construction of plasmids.
Plasmids carrying inserts from the
X. campestris pv. campestris
11 (strain Xc11) chromosome are depicted in Fig.
1. Plasmids
pBKE and pRKSE were previously constructed by cloning the 1.7-kb
EcoRI-
SstI fragment including the
blaXCC-1 gene and the N-terminal
region of
ampR1 into the
E. coli vector pOK12 and the broad-host-range
vector pRK415, respectively (
29). pBKX was obtained by cloning
the downstream
PstI-
SstI fragment from the pBKE insert into
pOK12 (
27). Using the labeled pBKX insert for hybridization,
pCH1 (with a ca. 4.0-kb insert) was obtained from a library
constructed by cloning the
Sau3A1 fragments from the Xc11 chromosome
into pOK12. Plasmid pFY13-9BSRX carried a 2.5-kb insert from
pCH1 containing the entire
ampR1 and
blaXCC-1 genes, cloned
in the
XbaI-
StuI sites of pFY13-9 (
14). Plasmid pFJ-ampR1 was
constructed by cloning the 1.3-kb
PstI-
XbaI fragment from the
pFY13-9BSRX insert, containing the entire
ampR1 gene, into the
broad-host-range vector pFJ9 (
7). Plasmid pOKSS was a derivative
of pOK12 carrying the 1.0-kb
SmaI-
SstI fragment from the pBKE
insert. Plasmid pBX contained the 500-bp
PstI-
PvuII DNA fragment
carrying the
blaXCC-1-
ampR1 IG (from the pFJ-ampR1 insert) with
the
blaXCC-1 promoter being situated in the same orientation
as and upstream of the
luxA and
luxB reporter genes in promoter-probing
vector pMY3 (
31). Plasmid pRX contained the same insert as that
of pBX except that the orientation was opposite, thus placing
the reporter genes under the control of the
ampR1 promoter.
Construction of the ampR1 mutant, Xc11RM.
Strain Xc11RM was constructed by insertional mutation. The 2.0-kb
tetracycline resistance (Tc
r) cartridge from mini-Tn
5Tc (
9)
was inserted into the
SalI site within
ampR1 of the pCH1 insert.
The resultant plasmid with the interrupted
ampR1 gene was then
electroporated into strain Xc11 to replace the chromosomal wild-type
version. One of the mutants (Xc11RM), resistant to tetracycline
and sensitive to ampicillin, thus obtained was verified to have
undergone a double crossover by Southern hybridization.
ß-Lactamase assays.
The activity of ß-lactamase was measured spectrophotometrically by monitoring the hydrolysis of nitrocefin (Calbiochem-Novabiochem Corp.) at room temperature as described previously (11), using the cell extracts prepared by sonication as the enzyme sources. One unit of enzyme was defined as the amount required to hydrolyze 1 nmol of nitrocefin per min. The protein contents were determined by the method of Bradford (4) with bovine serum albumin as the standard.
IEF analysis.
Isoelectric focusing (IEF) analysis of ß-lactamase in the crude extracts prepared from cultures of the Xanthomonas strains grown overnight was performed in PhastSystem (Amersham Biosciences) with precast gels (pI 3 to 9). The bands were visualized by overlaying the IEF gels with filter paper soaked in a 2.0-ml mixture prepared by combining 1.9 ml of 100 mM sodium phosphate buffer (pH 7.0) with 0.1 ml of nitrocefin (10 mg/ml in dimethyl sulfoxide).
Antibiotic sensitivity of Xanthomonas.
The MICs of different ß-lactam antibiotics for the Xanthomonas strains were determined by using Etest strips (AB Biodisk, Solna, Sweden) or by the microdilution method recommended by the National Committee for Clinical Laboratory Standards, using ß-lactams purchased from Sigma (St. Louis, Mo.). E. coli ATCC 25922 was used as the reference strain.
Primer extension.
A oligonucleotide primer with a sequence complementary to positions 80 to 104 downstream of the ampR1 start codon (5'-GCCTGGCTGACGCACAGCTCGCCGG-3'; designated primer R2) was radioactively labeled as previously described (30). Total RNA was isolated from cells of strain Xc11 grown to mid-exponential phase by the Qiagen RNA extraction system (Qiagen, Valencia, Calif.) according to the manufacturer's instructions. The reverse transcription was performed using the labeled primer and the extracted RNA (30 µg) as the template. The same primer was used for DNA sequencing on the insert of pOKSS (Fig. 1) at the same time to identify the positions of the transcriptional start sites.
DNA methods.
Preparation of plasmid and chromosomal DNA, restriction enzyme digestion, Southern blotting, and transformation of E. coli DH5
were performed by standard procedures (22). DNA sequences on both strands were determined by the dideoxy chain termination method (24). Plasmid was delivered to X. campestris by electroporation (28).
Luciferase activity determination.
Luciferase activity was assayed by measuring bioluminescence (in volts per milliliter) as described previously (15) by monitoring cell growth (from an optical density at 660 nm of approximately 0.05 to 2.0). The maximal values obtained from each culture were used for comparison.
Computer analysis.
The BLAST program was used to search the National Center for Biotechnology Information database for AmpR homologues. The dendrogram was constructed by using the Clustal X program.
Nucleotide sequence accession number.
The nucleotide sequence of 1,046 bp (from the blaXcc-1-ampR1 IG to the XmnI site) determined here has been deposited in GenBank under accession number AY165954.

RESULTS AND DISCUSSION
Sequence analysis of X. campestris pv. campestris ampR.
In our previous study of the
X. campestris strain Xc11 ß-lactamase
gene (
blaXCC-1), the sequence of the upstream region including
the N-terminal 41 codons of the regulatory
ampR1 gene was also
delineated (
29). In this study, the entire
ampR1 gene including
the region further upstream (Fig.
1) was sequenced. The relative
positions of the
blaXCC-1 and
ampR1 genes, contained within
the 2.5-kb
EcoRI-
XmnI fragment of the pFY13-9BSRX insert, are
shown in Fig.
1. Running opposite to
blaXCC-1, the Xc11
ampR1 gene encoded a polypeptide of 289 amino acid (aa) residues with
a calculated molecular size of 31 kDa, named AmpR1. Similar
to the situations of other
X. campestris chromosomal genes,
the
ampR1 gene had a G+C content of 70%, and G and C were strongly
favored at the third positions of the codons (79%). A region
having the potential to form a stem-loop structure that resembles
the transcriptional terminator was found 9 bp downstream from
the
ampR1 termination codon, spanning 27 nucleotides (nt) with
a calculated
G of -19.4 kcal/mol. There was no string of T residues
characteristic of typical Rho-independent transcriptional terminators
following the stem-loop structure.
Sequence comparisons of XCC and AmpR proteins.
A computer search revealed that the X. campestris pv. campestris ATCC 33913 genome had four ß-lactamase genes (synonym XCC3039, XCC2636, XCC2873, and XCC3197, encoding enzymes XCC-2, XCC-3, XCC-4, and XCC-5, respectively) and two ampR genes (synonym XCC3040 and XCC3781) (8). XCC3039 and XCC3040 were adjacent and running divergently, which suggests that they are cognate structural and regulatory genes. Sequence comparisons revealed that XCC-1 (295 aa) (29) and AmpR1 had 99 and 94% identity with XCC-2 (296 aa) and XCC3040 (291 aa), respectively. Low degrees of identity (29 to 35%) were shared between the amino acid sequences of the X. campestris paralogues, XCC-1 versus the other XCC proteins and AmpR1 versus XCC3781. These observations suggest that strain Xc11, the same pathovar as ATCC 33913, may also possess multiple bla genes. However, since mutation in blaXCC-1 renders the strain sensitive to ß-lactam antibiotics (29), the other blaXCC genes may not be required for resistance. One homologue to each of these Bla proteins was found in Xanthomonas axonopodis pv. citri 306 genome, XCC-6, XCC-7, XCC-8, and XCC-9 (8), which corresponded to XCC-2, XCC-3, XCC-4, and XCC-5 with 81, 86, 95, and 84% identities, respectively.
The AmpR1 protein also shared high degrees of identity with the X. axonopodis pv. citri 306 AmpR1 protein (synonym XAC3163; 81%), Pseudomonas aeruginosa AmpR (58.2%), and Burkholderia cepacia LysR (54.2%) and shared moderate degrees of identity (more than 45%) with several other bacterial AmpR proteins. However, although moderate to high degrees of identity were shared between these AmpR proteins, phylogenetic analysis revealed that the three AmpR1 proteins from Xanthomonas clustered independently and that the two AmpR2 proteins formed still another cluster, which was even further apart from the other clusters (Fig. 2). The low homology between AmpR1 and AmpR2 of the Xanthomonas strains suggests that they might be derived from different ancestors.
AmpR proteins are members of the LysR family of transcriptional
regulators that possess a helix-turn-helix motif at their N
terminus required for DNA binding (
25). With computer analysis
using NPS@, developed by PBIL Lyon-Gierland (
http://pbil.ibcp.fr/html/),
a helix-turn-helix motif was also found at the N-terminal region
in AmpR1 and XCC3040 (with the same sequence at the same position,
NLTRAAGELCVSQAALSHQIK, aa 22 to 42) and XCC3781 (NLSRAAAAMHLTVSALSHQVR,
aa 20 to 40).
The blaXCC-1-ampR1 IG contains partially overlapped promoters with low A+T content.
The bla-ampR IGs from nine strains of gram-negative bacteria were aligned with those of Xc11 and ATCC 33913 (Fig. 3). The blaXCC-1-ampR1 IG, with identical nucleotide sequence to and the same length (100 bp) as that of XCC3039-XCC3040, was shorter than the IG from other bacteria, which range from 127 to 151 bp (Fig. 3). Structural features typical of the bla-ampR IG present in other bacteria were also found in the blaXCC-1-ampR1 IG, including the conserved regions 1 and 2 predicted for AmpR binding and the LysR motif AN11T (Fig. 3). These IGs are commonly AT-rich and possess promoters with -10 and -35 sequences typical of E. coli
70 promoters. However, the A+T content in the X. campestris blaXCC-1-ampR1 IG was low (37%), and no regions conserved to the E. coli
70 promoters were found (Fig. 3). This latter finding is different from our previous observations that most of the X. campestris promoters are rich in A+T, in contrast to the overall low A+T content of the chromosome (31).
Sequence alignments suggested that the sequences 5'-AATGTT-3'
and 5'-CGGCGC-3' located 36 and 58 nt upstream of the
ampR initiation
codon with a 16-nt spacer between the two sequences are the
-10 and -35 sequences, respectively, of the
ampR1 promoter (Fig.
3). The same alignment suggested that the
blaXCC-1 promoter
had 3'-AGTATC-5' and 3'-CGACCA-5' (on the opposite strand) located
27 and 50 nt upstream of the
blaXCC-1 initiation codon as the
-10 and -35 sequences, respectively, suggesting that the
blaXCC-1 and
ampR1 promoter regions overlapped by 18 nt (Fig.
3).
Primer extension was performed to determine the transcription initiation site of ampR1. Extension reaction using primer R2 (5'-GCCTGGCTGACGCACAGCTCGCCGG-3'), complementary to nt 80 to 104 relative to the ampR initiation codon, yielded one extension product initiating with a G base that was 26 nt upstream from the ampR initiation codon and 9 nt downstream from the predicted -10 box (Fig. 4).
Expression of the blaXCC-1 gene is constitutive and requires the function of AmpR1.
MICs ranged from 4 (imipenem) to more than 256 µg/ml (ampicillin,
oxacillin, piperacillin-tazobactam, and carbenicillin) against
the Xc11 strain, while MICs decreased drastically against the
Xc11RM strain, with reductions ranging from 4 to 64 times lower
than the wild-type levels of resistance (Table
2). The wild-type
levels of resistance to ß-lactams were restored in
the mutant containing the cloned
ampR1 gene, Xc11RM(pFJ-ampR1)
(Table
2). Notably, the data indicated reduced susceptibility
to imipenem and resistance to cefoxitin similar to Xc11. These
are different from the situations with other class A ß-lactamases.
The reason remained to be studied. However, since XCC-1 shares
only 51.5% sequence identity with the
S. maltophilia L2 ß-lactamase
(
29), the most closely related class A enzyme, XCC-1 may have
varied hydrolytic properties for these substrates.
To test whether susceptibility to ß-lactams caused
by an
ampR1 mutation correlated with the loss of the responsible
enzymatic activity and whether expression of
blaXCC-1 can be
induced, ß-lactamase was assayed. Cultures were grown
to exponential phase (ca. 0.5 U of optical density at 550 nm)
without ß-lactams, divided into two parts, and grown
for 2 h with or without cefotaxime (8 µg/ml). In strain
Xc11RM, ß-lactamase activity was as low as 7 U/mg
of protein. Complementation of Xc11RM with pFJ-ampR1 restored
the enzyme activity (3,200 ± 44 U/mg), which was comparable
to that in the wild-type Xc11 (3,666 ± 80 U/mg) (Table
3). These results, demonstrating the activator function of AmpR,
indicate that a mutation in the
ampR1 gene caused a simultaneous
loss of the ß-lactamase activity, which in turn resulted
in susceptibility to ß-lactam antibiotics. The positive
control of AmpR1 over
blaXCC-1 expression is thus similar to
the
ampR-ampC system in
Enterobacteriaceae.
With cefotaxime, the enzyme levels in strains Xc11 (3,547 ±
144 U/mg) and Xc11RM(pFJ-ampR1) (3,122 ± 25 U/mg) were
about the same as those without cefotaxime (Table
3), suggesting
that the expression of
blaXCC-1 gene is constitutive and cannot
be further induced by cefotaxime. In the mutant cells (Xc11RM),
while the cells were not able to grow in the presence of cefotaxime,
no significant levels of ß-lactamase were detected
without cefotaxime either. In the parallel experiments using
Serratia marcescens 6 (strain Sm6) as a positive control, the
addition of 8 µg of cefotaxime per ml caused a fourfold
increase in the ß-lactamase activity (5,887 ±
147 versus 1,591 ± 71), suggesting that induction would
have been observed if it occurred in
Xanthomonas. In
Enterobacter,
Citrobacter, and
Pseudomonas, both hyperinducible and high-level
constitutive ß-lactamase production are due to mutations
in
ampD (
5,
13). Because an
ampD homologue is present in
X. campestris pv. campestris 33913 genome (
8), studies are in progress
to determine whether constitutive expression of
blaXCC-1 is
caused by a mutation in
ampD.
Several other Xanthomonas strains were also assayed for ß-lactamase levels, including X. axonopodis pv. vesicatoria 64 (strain Xv64), X. axonopodis pv. vesicatoria 3240 (strain Xv3240), X. campestris pv. campestris 6 (strain Xc6), X. campestris pv. campestris 17 (strain Xc17), and X. campestris pv. mangiferaeindcae 38 (strain Xcm38) (Table 3). As expected, the ampicillin-sensitive strains Xv3240 and Xcm38 did not produce significant levels of the enzyme. In contrast, the enzyme levels in strains Xc17 and Xc6 were similar to that in Xc11, whereas those in Xv64 were about threefold higher than that in Xc11. The addition of cefotaxime did not affect the levels of ß-lactamase in these strains, again suggesting that the enzyme is constitutively expressed. Since the ß-lactamase-producing strains were all wild-type bacteria, it appears that constitutive expression of ß-lactamase is intrinsic in Xanthomonas. Since Xanthomonas is a large genus and inhabits soil, infected plants, plant debris, and asymptomatic plants near acutely infected plants, constitutive expression of ß-lactamase by these bacteria raises environmental concerns regarding dissemination of the resistance gene.
To obtain ß-lactamase profiles, IEF was performed with crude extracts prepared from strains including Xc11, Xc11RM, Xc11RM(pFJ-ampR1), 11bla::Tc, 11bla::Tc(pRKSE), Xc6, Xc17, Xv64, and Xcm38. A single band was localized near pI 8.2, similar to that predicted for XCC-1 (29), in all strains grown with or without cefotaxime, except in strains 11bla::Tc, Xcm38, and Xc11RM which did not display significant levels of ß-lactamase (data not shown). These data indicated the existence of only one species of ß-lactamase in each of these strains. Notably, Xv64 displayed a band with much stronger intensity than those of the other strains (data not shown), consistent with the data that Xv64 exhibited threefold-higher levels of ß-lactamase than Xc11.
The ampR1 promoter is not active in E. coli.
Because the A+T content of the blaXCC-1-ampR1 IG was low, which differs from the typical
70 promoters, we were curious about whether the promoters were able to express in E. coli. For the test, plasmid pFY13-9BSRX (Fig. 1) carrying the entire ampR1 and blaXCC-1 genes was introduced into E. coli DH5
. The transformant, E. coli(pFY13-9BSRX), was resistant to kanamycin but unable to grow in L agar plate containing ampicillin, indicating that while the plasmid-encoded kanamycin resistance was functional, ß-lactamase was not produced by the cloned blaXCC-1 gene in E. coli. Results of enzyme assays confirmed that no significant levels of ß-lactamase activity were present.
Reporter plasmids pBX and pRX with transcriptional fusions (Fig. 1) were used to assay for the blaXCC-1 and ampR1 promoter activities, respectively. No significant levels of luciferase activity were detected in either of the constructs, indicating that both blaXCC-1 and ampR1 promoters were not active. The observation that ampR1 promoter is not expressed is consistent with our previous report that most of the Xanthomonas promoters are not expressed in E. coli (31). Since expression of the blaXCC-1 promoter requires AmpR1, no expression of Xc11 blaXCC-1-ampR1 system in E. coli is thus explained.
Distribution of the ampR gene in xanthomonads.
We have previously shown that 13 Xanthomonas strains tested, except Xcm38, are all resistant to ampicillin and contain a bla gene detectable by Southern hybridization (29). In this study, the labeled 240-bp PvuII-SalI DNA fragment within the ampR1 gene was used as a probe for Southern hybridization with the EcoRI-digested chromosomal DNA from these Xanthomonas strains. We detected a 3.8-kb fragment in X. campestris pathovars campestris (Xc2, Xc6, Xc11, Xc11A, Xc17, and Xc85), begoniae (Xcb59), dieffenbachiae (Xcd65), and phaseoli (Xcp73), a 10-kb fragment in X. axonopodis pathovars citri (Xac60), glycines (Xcg69), and vesicatoria (Xv64), and a 5.5-kb fragment in X. oryzae pv. oryzae (Xo21), but none in the ampicillin-sensitive Xcm38 (data not shown). These observations together indicate that each of the ampicillin-resistant Xanthomonas strains contains genes homologous to blaXCC-1 and ampR1.

ACKNOWLEDGMENTS
This study was supported in part by grant NSC-90-2311-B005-025
from the National Science Council and grant 91-B-FA05-1-4AA91002A
of the Program for Promoting Academic Excellence of Universities
from the Ministry of Education of the Republic of China.

FOOTNOTES
* Corresponding author. Mailing address: Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan, Republic of China. Phone: 886-4-2285-1885. Fax: 886-4-2287-4879. E-mail:
yhtseng{at}dragon.nchu.edu.tw.


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Antimicrobial Agents and Chemotherapy, January 2004, p. 209-215, Vol. 48, No. 1
0066-4804/04/$08.00+0 DOI: 10.1128/AAC.48.1.209-215.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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