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Antimicrobial Agents and Chemotherapy, November 2000, p. 3003-3007, Vol. 44, No. 11
0066-4804/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.
Purification and Biochemical Characterization of
the VIM-1 Metallo-
-Lactamase
Nicola
Franceschini,1,*
Berardo
Caravelli,1
Jean-Denis
Docquier,2
Moreno
Galleni,3
Jean-Marie
Frère,3
Gianfranco
Amicosante,1 and
Gian
Maria
Rossolini2,*
Dipartimento di Scienze e Tecnologie
Biomediche, Università degli Studi L'Aquila, I-67100 Coppito,
L'Aquila,1 and Dipartimento di Biologia
Molecolare, Sez. di Microbiologia, Università di Siena, I-53100
Siena,2 Italy, and Laboratoire
d'Enzymologie et Centre d'Ingénierie des Protéines,
Institut de Chimie, Université de Liège, Sart Tilman,
B-4000 Liège, Belgium3
Received 13 January 2000/Returned for modification 5 May
2000/Accepted 8 August 2000
 |
ABSTRACT |
VIM-1 is a new group 3 metallo-
-lactamase recently detected in
carbapenem-resistant nosocomial isolates of Pseudomonas
aeruginosa from the Mediterranean area. In this work, VIM-1 was
purified from an Escherichia coli strain carrying the
cloned blaVIM-1 gene by means of an
anion-exchange chromatography step followed by a gel permeation
chromatography step. The purified enzyme exhibited a molecular mass of
26 kDa in sodium dodecyl sulfate-polyacrylamide gel electrophoresis,
and an acidic pI of 5.1 in analytical isoelectric focusing.
Amino-terminal sequencing showed that mature VIM-1 results from the
removal of a 26-amino-acid signal peptide from the precursor. VIM-1
hydrolyzes a broad array of
-lactam compounds, including penicillins, narrow- to expanded-spectrum cephalosporins, carbapenems, and mechanism-based serine-
-lactamase inactivators. Only monobactams escape hydrolysis. The highest catalytic
constant/Km ratios (>106
M
1 · s
1) were observed with
carbenicillin, azlocillin, some cephalosporins (cephaloridine,
cephalothin, cefuroxime, cefepime, and cefpirome), imipenem, and
biapenem. Kinetic parameters showed remarkable variability with
different
-lactams and also within the various penam, cephem, and
carbapenem compounds, resulting in no clear preference of the enzyme
for any of these
-lactam subfamilies. Significant differences were
observed with some substrates between the kinetic parameters of VIM-1
and those of other metallo-
-lactamases. Inactivation assays carried
out with various chelating agents (EDTA,
1,10-o-phenanthroline, and pyridine-2,6-dicarboxylic acid)
indicated that formation of a ternary enzyme-metal-chelator complex
precedes metal removal from the zinc center of the protein and revealed
notable differences in the inactivation parameters of VIM-1 with
different agents.
 |
INTRODUCTION |
Production of
-lactamases is the
most common mechanism of bacterial resistance to
-lactam
antibiotics. Among the
-lactam-degrading enzymes,
metallo-
-lactamases are notable for their substrate profile, which
always includes carbapenems and often most classes of
-lactams, and
for their resistance to mechanism-based
-lactamase inactivators
(3, 4, 20). Owing to these features, the emergence of
acquired metallo-
-lactamases in clinical isolates of major
gram-negative pathogens, such as members of the family Enterobacteriaceae and Pseudomonas aeruginosa, is
a most worrying development in the field of microbial drug resistance
(12).
VIM-1 is a new molecular class B metallo-
-lactamase which has
recently been identified in carbapenem-resistant isolates of Pseudomonas aeruginosa from various Italian hospitals
(11, 13, 21) and from Greece (27). Like the
blaIMP gene, which was the first acquired
metallo-
-lactamase determinant found in nosocomial isolates of
various gram-negative species in Japan (1, 7, 8, 16, 24,
25) and, more recently, even outside Japan (G. Cornaglia, M. L. Riccio, A. Mazzariol, P. Piccoli, L. Lauretti, R. Fontana, and G. M. Rossolini, Letter, Lancet
353:899-900; T. H. Koh, G. S. Babini, N. Woodford, L. H. Sng, L. M. Hall, and D. M. Livermore,
Letter, Lancet 353:2162; K. Lee, Y. Chong, H. B. Shin,
and D. Yong, Abstr. 38th Intersci. Conf. Antimicrob. Agents Chemother.,
abstr. E-85, p. 193, 1998), the blaVIM-1 gene is
carried on an integron-borne gene cassette (11) and has the potential for spreading among major bacterial pathogens. For this reason, blaVIM-1 is potentially a very dangerous
resistance determinant from the clinical standpoint.
In this work, a protocol for purification of the VIM-1 enzyme was
developed, and the functional properties of the purified enzyme were investigated.
 |
MATERIALS AND METHODS |
Purification of VIM-1.
The VIM-1 enzyme was purified from
Escherichia coli(pBCLL/39H) (11) grown
aerobically in 2 liters of brain heart infusion broth (Difco
Laboratories, Detroit, Mich.) containing chloramphenicol (60 µg/ml)
for 18 h at 37°C. The cells were harvested by centrifugation, washed twice with 30 mM sodium cacodylate buffer (pH 6.3), resuspended in 100 ml of the same buffer supplemented with 100 µM
ZnCl2 (CBZ), and disrupted by sonication (five times for
30 s each time at 60 W). Cell debris was removed by high-speed
centrifugation (105,000 × g for 60 min at 4°C), and
the clarified supernatant was loaded on a Q-Sepharose FF column (2.6 by
26 cm; Amersham-Pharmacia Biotech, Uppsala, Sweden) previously
equilibrated with CBZ. After the column was washed with the same
buffer, the bound proteins were eluted by a linear NaCl gradient (0 to
0.7 M) in CBZ (flow rate, 3 ml/min). The fractions containing
carbapenemase activity were pooled, dialyzed against 30 mM HEPES buffer
(pH 7.5), concentrated 10-fold by ultrafiltration, and loaded on a
Superdex 75 column (1.6 by 75 cm; Amersham-Pharmacia Biotech)
equilibrated and eluted with 30 mM HEPES (pH 7.5). The
-lactamase-containing elution peak was concentrated at 1 mg/ml by
ultrafiltration and stored at
80°C until it was used. The protein
concentration in solution was assayed with a commercial kit (Bio-Rad
[Richmond, Calif.] protein assay), with bovine serum albumin used as
a standard.
During the purification procedure the presence of carbapenemase
activity was monitored using 100 µM meropenem as a substrate in 30 mM
HEPES (pH 7.5) at 30°C.
Protein electrophoretic techniques.
Sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed
according to the method of Laemmli (9) using final
acrylamide concentrations of 12 and 5% (wt/vol) for the separating and
stacking gels, respectively. After electrophoresis, the protein bands
were stained with Coomassie brilliant blue R-250. Analytical
isoelectric focusing of the purified protein was performed in a precast
polyacrylamide gel containing ampholites (pH range, 3.5 to 9.5)
(Ampholine PAGplate; Amersham Pharmacia Biotech) using a Multiphor II
Apparatus (Pharmacia-LKB, Uppsala, Sweden). The gels were focused at
0.1 W/cm2 for 3 h at 10°C. The
-lactamase
activity was revealed by overlaying the gel with a filter paper soaked
with 0.25 mM nitrocefin (Unipath, Milan, Italy) as described previously
(11).
N-terminal sequencing.
The N-terminal sequence of the
purified VIM-1 protein was determined using a gas phase sequencer
(Procise-492; Applied Biosystems, Foster City, Calif.) after
resuspension of the protein (50 pmol) in a 0.1% (vol/vol)
trifluoroacetic acid solution and loading the sample onto a
polyvinylidene difluoride membrane (Millipore Corp., Bedford, Mass.).
Determination of kinetic parameters.
Substrate hydrolysis by
the purified enzyme was monitored by following the absorbance variation
at 30°C, using a lambda 2 spectrophotometer (Perkin-Elmer, Rahway,
N.J.) equipped with thermostatically controlled cells. Azlocillin was
from Sigma Chemical Co. (St. Louis, Mo.), and mezlocillin was from
Bayer AG (Leverkusen, Germany). The wavelengths and changes in
extinction coefficients used in the spectrophotometric assays were 240 nm and
1,130 M
1 cm
1 with azlocillin and
235 nm and
1,100 M
1 cm
1 with mezlocillin.
For other
-lactam compounds, the sources and the wavelengths and
changes in extinction coefficients used in the spectrophotometric
assays were as described previously (10, 19). The
experimental conditions (reaction buffer and volume) used in the
spectrophotometric assays were as described previously (10).
The steady-state kinetic parameters (Km and
catalytic constant [kcat]) were determined
under initial-rate conditions using the Hanes-Woolf plot
(23). Km values lower than 20 µM were measured as inhibition constants (Kis) in a
competitive model, using 50 µM nitrocefin as the reporter substrate.
The Ki value was determined by the plot of Vo/Vi
versus I, yielding a line whose slope is
Kms/(Kms + S) · Ki, where Vo and Vi are the
initial rates of nitrocefin hydrolysis in the absence and presence of
the inhibitor, respectively, I is the inhibitor
concentration, S is the reporter substrate concentration,
and Kms the Michaelis constant of
the enzyme for the reporter substrate.
Inactivation by chelating agents.
Inactivation of VIM-1 by
divalent ion chelators was studied in 50 mM HEPES (pH 7.5) at 30°C,
using 50 µM nitrocefin as the reporter substrate, in the presence of
different concentrations of EDTA, 1,10-o-phenanthroline, and
pyridine-2,6-dicarboxylic (dipicolinic) acid (Sigma) in a total volume
of 0.5 ml. Since the inactivation time courses followed
pseudo-first-order kinetics, the rate constants characterizing the
inactivation of the enzyme were calculated from the dependence of the
pseudo-first-order constant ki upon the
chelating agent concentration on the basis of the following
model:
Kk+2
E · Zn + C
E · Zn · C
E + Zn · C,
in which E · Zn, C, E · Zn · C, E,
and Zn · C are the metalloenzyme, the chelator, a ternary
metalloenzyme-chelator complex,
the apoenzyme, and the metal-chelator
complex, respectively;
K represents the dissociation
constant of the E · Zn · C ternary
complex; and
k+2 is the individual rate constant for the
dissociation of E · Zn · C into E + Zn · C, a
step which, under
our experimental conditions, appeared to be
essentially irreversible.
The individual values of
K and
k+2 were determined by fitting
the value of
ki, the pseudo-first-order inactivation rate
constant,
to the equation
where [S] and
Kms were the
concentration and the
Km value of the reporter
substrate,
respectively.
 |
RESULTS |
Purification and structural properties of the VIM-1 enzyme.
The VIM-1 enzyme was purified from a lysate of E. coli
DH5
(pBCLL/39H), which carries the cloned
blaVIM-1 gene on a multicopy plasmid vector
(11), by means of an anion-exchange chromatography step on
Q-Sepharose followed by a gel permeation chromatography step on
Superdex 75. Approximately 1.15 mg of purified enzyme was obtained per
liter of culture using the above-described protocol. The degree of
purity, evaluated by SDS-PAGE, was higher than 95% (Fig.
1), and the overall yield of the
purification protocol was 17% (Table 1).

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|
FIG. 1.
SDS-PAGE analysis of the fractions containing
carbapenemase activity eluted from the Q-Sepharose FF columns (Q-FF)
and from the Superdex 75 column (S-75). Protein mass standards are
reported in kilodaltons on the left.
|
|
In SDS-PAGE, the VIM-1 polypeptide migrated with an apparent
molecular mass of approximately 26 kDa (Fig.
1). The isoelectric
pH of
purified VIM-1, determined by analytical isoelectric focusing,
was 5.1 (data not shown). The N-terminal sequence of purified
VIM-1 was
found to be NH
2-GEPSG, indicating that mature VIM-1
is
generated following the cleavage of a 26-amino-acid signal
peptide from
the precursor (
11). According to this information,
and
assuming no further posttranslational modification, the calculated
molecular mass of VIM-1 is 25,322
Da.
Kinetic parameters of VIM-1 with various
-lactam compounds.
The kinetic parameters of VIM-1, including Km,
kcat, and the
kcat/Km ratio, were
determined with several different
-lactam compounds.
Under the experimental conditions adopted, the enzyme hydrolyzed all
the tested compounds except aztreonam (Table
2). Individual
kinetic parameters were
remarkably variable for different

-lactams,
with up to 1,000-fold
differences in the values of
Km,
kcat, and
the
kcat/
Km ratio. The
highest values of the
kcat/
Km ratio
(>10
6 M
1 · s
1) were
found with carbenicillin, azlocillin, imipenem, biapenem,
and some
cephalosporins (nitrocefin, cephaloridine, cephalothin,
cefuroxime, cefepime, and cefpirome). The lowest values of the
kcat/
Km ratio
(<10
5 M
1 · s
1)
were observed with penicillin G, ampicillin, temocillin, ceftazidime,
and the serine-

-lactamase inactivators sulbactam, tazobactam,
and

-iodopenicillanate. Considerable variability was observed
within the various

-lactam subfamilies (penam, cephem, and
carbapenem
compounds), resulting in no clear preference of VIM-1
for any
of these groups (Table
2). Among carbapenems, VIM-1 exhibited
relatively low
kcat values but very high
affinities for imipenem
and biapenem, eventually resulting in
high
kcat/
Km ratios
(Table
2). This behavior was quite different from that of other
metallo-

-lactamases
(Table
3).
Interaction of VIM-1 with chelating agents.
The activity of
VIM-1 was inhibited by chelating agents, including EDTA,
1-10-o-phenanthroline, and dipicolinic acid. The inactivation time courses followed pseudo-first-order kinetics, and the
inactivation rates increased with the chelating agent concentrations in
a hyperbolic manner (data not shown). This indicated that the
above-mentioned compounds did not act by simply scavenging the free
metal ions and that the formation of a ternary enzyme-metal-chelator complex precedes the removal of the metal from the zinc center of the protein.
Although the models of the enzyme interaction with chelators were
similar, a remarkable variability was observed in the inactivation
parameters of different agents, with EDTA behaving as a poor
inactivator
and 1,10-
o-phenanthroline apparently being the
most efficient
inactivator (Table
4).
 |
DISCUSSION |
Results of this study showed that VIM-1 exhibits an exceedingly
broad substrate specificity, which includes virtually all
-lactams
except monobactams. Based on these properties, therefore, VIM-1 can be
assigned to subgroup 3a of group 3 of the functional classification of
-lactamases (3, 4, 20). This behavior emphasizes the
clinical significance of this new mobile
-lactamase.
Determination of the kinetic parameters of the purified enzyme with
several substrates allowed us to make comparisons with other
metallo-
-lactamases and revealed some interesting features of VIM-1.
In penicillins, the structure of the C-6 side chain apparently exerts a
remarkable influence on the substrate susceptibility to the enzyme. In
fact, carbenicillin behaved as a good substrate, while hydrolysis of
penicillin G and ampicillin was approximately 50-fold less efficient
(Table 2). This behavior is quite different from that of IMP-1, which
exhibits a marked preference for penicillin G and ampicillin compared
to carboxy-penicillins (10), and also from that of the
Bc-II, CcrA, and L1 enzymes, which hydrolyze the above-mentioned
compounds with similar efficiencies (6, 31). Another
relevant difference was observed with temocillin, which was recognized
with a relatively high affinity and hydrolyzed by VIM-1 (Table 2) but
is not a substrate for either IMP-1 (10) or Bc-II
(5). The activity of VIM-1 on temocillin was confirmed by
the fact that the MIC of temocillin for E. coli
DH5
(pBCLL/39H), which carries a recombinant plasmid containing the
blaVIM-1 cassette and produces the VIM-1 enzyme
(11), is increased remarkably compared to that for DH5
harboring the empty cloning vector (>256 versus 8 µg/ml) (G. M. Rossolini, M. L. Riccio, and J.-D. Docquier, unpublished results).
This indicates that the presence of an
-methoxy group at position
C-6 does not prevent the interaction of penicillins with VIM-1.
Cephalosporins were usually good substrates for VIM-1
(values of kcat/Km were
often higher than 106 M
1 · s
1), with somewhat lower efficiencies being observed with
oxymino-cephalosporins (cefotaxime and ceftazidime) and cefoxitin
(Table 2). The difference in the kinetic constants of cephalothin
and cefoxitin suggests that the presence of an
-methoxy group at
position C-7 reduces the susceptibility of cephalosporins to VIM-1,
although it does not prevent interaction and hydrolysis. Again, this
behavior is different from that of IMP-1, which is not affected by the
presence of an
-methoxy group at position C-7 (10), while
it resembles that of Bc-II, which, however, is more severely affected
by this type of modification (6).
Also, carbapenems were good substrates for VIM-1 (Table 2), with values
of kcat/Km overall
similar to those reported for other metallo-
-lactamases (Table 3).
Interestingly, the highly efficient degradation of imipenem by VIM-1
(kcat/Km,
106 M
1 · s
1) was
dependent on a very high affinity for the substrate associated with
relatively low turnover rates, which is a strategy different from
that adopted by the other group 3 enzymes, which exhibit comparable kcat/Km ratios
resulting from higher turnover rates and remarkably lower affinities
(Table 3).
Most recently, an allelic variant of the
blaVIM-1 gene, named
blaVIM-2, whose product exhibits 93% amino acid
identity to mature VIM-1, was identified in a P. aeruginosa
clinical isolate from France (18) and in P. aeruginosa clinical isolates from Italy (Rossolini et al.,
unpublished). Comparison of the kinetic parameters of VIM-1 determined
in this work with those reported for VIM-2 (18) revealed
similar kcat/Km ratios
with several substrates (carbapenems, piperacillin, ticarcillin,
narrow-spectrum cephalosporins, and cefotaxime) but notable differences
with penicillin G, cefuroxime, ceftazidime, cefepime, and cefpirome
(compared to those reported for VIM-2, the
kcat/Km ratios of VIM-1
with these substrates were 34-fold lower, 14-fold higher, 12-fold
lower, 127-fold higher, and 36-fold higher, respectively). This
suggests that at least some of the structural differences between VIM-1 and VIM-2 could be functionally relevant, although a comparative kinetic analysis of the two enzymes under identical experimental conditions would be necessary for a definitive confirmation.
The mode of interaction of VIM-1 with chelating agents appeared to
follow a mechanism similar to that observed with other metallo-
-lactamases (10, 22), in which the formation
of a ternary enzyme-metal-chelator complex precedes the removal of the metal from the zinc center of the protein. Similar to other group 3 enzymes (10, 22), VIM-1 appeared to be more susceptible to
1,10-o-phenanthroline and dipicolinic acid than to EDTA.
However, unlike BlaB and IMP-1, which are overall more susceptible to
dipicolinic acid than to 1,10-o-phenanthroline (10,
22), VIM-1 appeared to be more susceptible to the latter agent.
The potential clinical significance of VIM-1 and the uniqueness of some
of its functional properties render this enzyme a most interesting
candidate for further studies of the molecular structure and the
interaction with known metallo-
-lactamase inhibitors (14, 17,
26, 29).
 |
ACKNOWLEDGMENTS |
This work was supported by the European research network on
metallo-
-lactamases within the Training and Mobility of Researchers (TMR) Program (contract no. FMRX-CT98-0232) and by grant no. 9906404271 from MURST ex-40%.
 |
FOOTNOTES |
*
Corresponding author. Mailing address for Nicola
Franceschini: Dipartimento di Scienze e Tecnologie Biomediche,
Università degli Studi de L'Aquila, Via Vetoio, 67100 L'Aquila,
Italy. Phone: 39 0862 433456. Fax: 39 0862 433433. E-mail:
nicola.franceschini{at}cc.univaq.it.
Mailing address for Gian Maria Rossolini: Dipartimento di Biologia
Molecolare, Sez. di Microbiologia, Università di Siena, Via
Laterina, 8, 53100-Siena, Italy. Phone: 39 0577 233327. Fax: 39 0577 233325. E-mail: rossolini{at}unisi.it.
 |
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Antimicrobial Agents and Chemotherapy, November 2000, p. 3003-3007, Vol. 44, No. 11
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Copyright © 2000, American Society for Microbiology. All rights reserved.
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