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Antimicrobial Agents and Chemotherapy, December 2004, p. 4778-4783, Vol. 48, No. 12
0066-4804/04/$08.00+0 DOI: 10.1128/AAC.48.12.4778-4783.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Teresa Lopizzo,1
Sabrina Liberatori,2
Manuela Prenna,3
Maria Cristina Thaller,4
Jean-Marie Frère,5 and
Gian Maria Rossolini1*
Dipartimento di Biologia Molecolare, Laboratorio di Fisiologia e Biotecnologia dei Microrganismi,1 Laboratorio di Proteomica Funzionale, Università di Siena, Siena,2 Dipartimento di Biologia Molecolare, Cellulare e Animale, Università di Camerino, Camerino,3 Dipartimento di Biologia, Università di Roma "Tor Vergata," Rome, Italy,4 Laboratoire d'Enzymologie and Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, Liège, Belgium5
Received 21 January 2004/ Returned for modification 8 May 2004/ Accepted 4 August 2004
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MBLs belong to molecular class B (1) and constitute a family of very diverse enzymes. Based on structural relatedness, they can be grouped into three different subclasses: B1, B2, and B3 (14, 23). Subclass B3, originally represented by the L1 enzyme from Stenotrophomonas maltophilia (4, 26), has recently expanded to include several enzymes from primarily environmental bacteria (FEZ from Legionella gormanii [5], GOB from Chryseobacterium meningosepticum [3], THIN-B from Janthinobacterium lividum [25], and CAU from Caulobacter crescentus [9]), some of which can occasionally behave as opportunistic pathogens. The MBLs of subclass B3 are highly divergent from those of subclass B1 at the sequence level (14) and, although they retain a three-dimensional fold that is similar overall, exhibit an organization of the metal-binding sites that differs significantly from that of enzymes of subclass B1 (15, 28).
The THIN-B enzyme from J. lividum was identified following an environmental screening of MBL-producing bacteria (25) and currently is the only known MBL from a member of the ß-Proteobacteria class. Compared to the other enzymes of subclass B3, THIN-B is quite divergent and exhibits some unique structural features, including a larger size and a higher number of cysteine residues (25). However, the biochemical properties of this enzyme have not been investigated.
In this paper we describe a system for overproduction of the THIN-B enzyme in Escherichia coli, the protocol for purification of the recombinant protein, and the biochemical and kinetic characterization of THIN-B.
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lacZWJ16 hsdR514
araBA-DAH33
rhaBADLD78
pyrC (
cIts857 ind1 Sam7 nin5 lacUV5-T7 gene 1)]} (constructed in our laboratory) were used as hosts for T7 promoter-based expression plasmids for blaTHIN-B overexpression experiments. Media and culture conditions. Bacteria were always grown aerobically at 37°C unless otherwise specified. Luria-Bertani medium (27) was routinely used for the propagation of E. coli strains. SB medium (20 g of yeast extract/liter, 35 g of tryptone/liter, and 5 g of NaCl/liter; buffered with 50 mM sodium phosphate buffer [pH 7.0]) was used in overexpression experiments with BL21(DE3) and MCT236(DE3) strains. LBON (5 g of yeast extract/liter and 10 g of tryptone/liter) was used in overexpression experiments with BL21-SI.
Recombinant DNA methodologies. The open reading frame encoding THIN-B was amplified by PCR using primers THIN-B-EXP/f (5'-CAT ATG ACA CTA TTG GCG AAG TTG ATG CTG), which added an NdeI linker (boldfaced) to the 5' end, and THIN-B-EXP/r (5'-GGA TCC TAG TGC GCG TGC TGG G), which added a BamHI linker (boldfaced) to the 3' end. PCR was performed in a volume of 50 µl, with 3.5 U of the Expand High Fidelity PCR system (Roche Biochemicals, Mannheim, Germany) in the buffer provided by the manufacturer, 200 µM deoxynucleoside triphosphates, 50 pmol of each primer, and 10 ng of plasmid pBCIRO-K (25) as the template for the blaTHIN-B gene. The following cycling conditions were used: initial denaturation at 94°C for 3 min; denaturation at 94°C for 60 s, annealing at 58°C for 60 s, and extension at 72°C for 90 s, repeated for 30 cycles; and a final extension step at 72°C for 10 min. The amplified DNA was cloned into the SmaI site of plasmid pUC-18 by using the Sure Cloning kit (Amersham Biosciences, Uppsala, Sweden), yielding the recombinant plasmid pUC-CIRO. Finally, the 0.95-kb NdeI-BamHI fragment of pUC-CIRO, containing the blaTHIN-B gene, was subcloned into the pET-9a expression vector to produce the recombinant plasmid pET-THIN-B. The cloned blaTHIN-B gene was sequenced to rule out the presence of any PCR-generated mutations.
Expression experiments.
THIN-B production was tested by using three different expression systems, obtained by transformation of E. coli BL21(DE3), BL21-SI, or MCT236(DE3) with pET-THIN-B. With each system MBL production was monitored, over a 24 h time course, in both supernatants and cell extracts of cultures growing in SB medium containing 50 µg of kanamycin/ml at either 25 or 37°C. Individual cultures were incubated until the A600 reached 0.8 and then were split into two identical flasks, to one of which was added 1 mM isopropyl-ß-D-thiogalactopyranoside (IPTG) [for the BL21(DE3) and MCT236(DE3) hosts] or 0.3 M NaCl (for the BL21-SI host). Aliquots (1 ml) were sampled at different times and centrifuged (12,000 x g, 5 min, 4°C), and the culture supernatant was stored at 4°C. The bacterial pellet was resuspended in 1 ml of 10 mM HEPES-NaOH (pH 7.5) supplemented with 50 µM ZnSO4 and was disrupted by sonication (5 cycles, for 20 s each cycle, at 45 W) using a B. Braun (Melsungen, Germany) Labsonic L sonicator. The supernatant obtained after centrifugation at 10,000 x g for 15 min, to remove cell debris, represented the cell extract. MBL activities in supernatants and cell extracts were determined spectrophotometrically at 30°C by using 150 µM imipenem as the substrate (wavelength, 300 nm; 
, 9,000 M1 · cm1) in 10 mM HEPES-NaOH buffer (pH 7.5) (20). The reaction volume was 500 µl.
Purification of the THIN-B enzyme. The THIN-B MBL was purified from a culture of E. coli MCT236(DE3)(pET-THIN-B) grown in 0.5 liter of SB medium at 25°C. The culture was induced with 1 mM IPTG when the A600 was equal to 0.8. Cells were collected, 24 h after induction, by centrifugation (10,000 x g, 15 min, 4°C), resuspended in 20 ml of 20 mM ethanolamine-NaOH buffer (pH 9.8) containing 1 mM MgCl2 and 50 µM ZnSO4, and disrupted by sonication as described above. Cellular debris was removed by centrifugation (12,000 x g, 60 min, 4°C). The cleared supernatant was desalted by using a HiPrep 26/10 desalting column (Amersham Biosciences) and loaded (flow rate, 2 ml/min) onto an HR column (1.6 by 5 cm) packed with 10 ml of Source 15Q (Amersham Biosciences), equilibrated with 20 mM ethanolamine-NaOH buffer (pH 9.8) (buffer A). Proteins were eluted (flow rate, 4 ml/min) by using a linear gradient of NaCl (0 to 0.2 M, in 40 ml) in buffer A. Fractions exhibiting imipenemase activity were pooled and concentrated by ultrafiltration using a Centriprep YM10 filter unit (Millipore, Bedford, Mass.), and the buffer was changed to 50 mM sodium acetate buffer (pH 5.0) (buffer B) by using a PD-10 disposable column (Amersham Biosciences). The sample was then loaded (flow rate, 1 ml/min) onto a Resource S column (6.4 by 30 mm; Amersham Biosciences) preequilibrated with buffer B and was eluted by using a linear NaCl gradient in buffer B (0 to 1 M, in 20 ml). Fractions exhibiting the highest imipenemase activity were pooled, and the buffer was changed to 50 mM HEPES-NaOH (pH 7.5) containing 50 µM ZnSO4 (HBZ buffer), as above. The purified enzyme was stored in HBZ buffer at 80°C until use. During purification, imipenemase activity was assayed as described for expression experiments (see preceding section).
Protein analysis techniques. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) was performed by the method of Laemmli (18) by using a 12% acrylamide concentration in the resolving gel. After electrophoresis, protein bands were stained with Coomassie brilliant blue. Analytical isoelectric focusing (IEF) of the purified protein and zymographic detection of ß-lactamase activity were carried out as described previously (21). The molecular mass of native THIN-B was estimated by size exclusion chromatography using a Superdex 75 HR 10/30 column (Amersham Biosciences) as described previously (9, 10). The column was calibrated by using a mixture of bovine serum albumin (0.2 mg), ovalbumin (0.2 mg), chymotrypsinogen A (0.2 mg), and RNase A (0.5 mg). The protein concentration in solution was determined by using a commercial kit (Bio-Rad [Richmond, Calif.] protein assay) with bovine serum albumin as the standard. The BBL numbering scheme (14) is used throughout this paper.
Mass spectrometry. The mass of the purified THIN-B protein was measured by using an Ettan MALDI-TOF Pro mass spectrometer (Amersham Biosciences). The enzyme preparation had previously been desalted by using a ZipTip C4 (Millipore Corporation). Protein identification by mass spectrometry was achieved by peptide mass fingerprinting (PMF) (17). Briefly, the purified THIN-B protein was digested in 50 mM NH4HCO3 buffer (pH 7.0) by using trypsin (Promega, Madison, Wisc.) at a final protease/protein ratio of 1:50; the reaction took place at 37°C for 1 h. The mass spectra of the peptides in the mixture were acquired by using an Ettan MALDI-TOF Pro mass spectrometer (Amersham Biosciences), and the experimental data were compared to theoretical PMFs calculated for all the sequences in DNA and protein sequence databases by using the database search engine MASCOT, available online (http://www.matrixscience.com).
Determination of kinetic parameters.
The steady-state kinetic parameters for ß-lactam hydrolysis were measured in HBZ buffer at 30°C as described previously (9, 10). Competition experiments with aztreonam were carried out by using 200 µM imipenem as the reporter substrate and aztreonam concentrations up to 1 mM. Inactivation rates (ki) with divalent metal chelators were determined as described previously (10) in 50 mM HEPES-NaOH buffer (pH 7.5) (HB buffer) at 30°C by using 1 mM meropenem as the reporter substrate. Data were analyzed as described previously (16) according to the following scheme:
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to the experimental data, where k2' is k2 · [Zn · C] and K' is
, where KmS is the Km for the reporter substrate (16). The enzyme concentration in kinetic assays ranged between 3.5 and 95 nM. Determination of free sulfhydryl groups in the protein. The free sulfhydryl groups were titrated in unfolded purified protein samples (after addition of 6 M guanidinium chloride), in either unreduced or reduced forms, by using Ellman's assay, as described previously (7). The reduced form was obtained after incubation of the protein in the presence of 10 mM dithiothreitol for 1 h at 20°C and subsequent removal of the excess reducer by desalting the sample by use of a PD-10 column (Amersham Biosciences). The final enzyme concentration in the assay was 0.1 mg/ml.
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FIG. 1. Time-dependent production of the THIN-B enzyme in cell lysates with different expression systems. E. coli BL21(DE3)(pET-THIN-B), white; E. coli BL21-SI(pET-THIN-B), light grey; E. coli MCT236(DE3)(pET-THIN-B), dark grey. Hatched bars represent samples from cultures to which an inducer (1 mM IPTG, or 0.3 M NaCl for BL21-SI) was added.
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TABLE 1. Summary of a typical purification procedure of the THIN-B enzyme from E. coli MCT236(DE3)(pET-THIN-B)
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TABLE 2. MALDI-TOF mass spectrum data obtained for the THIN-B protein preparation after digestion with trypsina
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Size exclusion chromatography yielded a molecular mass of 32 ± 2 kDa, indicating that, under the experimental conditions adopted, the native enzyme is monomeric, unlike L1 but like most other MBLs (3, 4, 9, 22). The absence of oligomerization in THIN-B, despite its longer N-terminal portion, is consistent with the absence of the residues that are known to be involved in oligomerization of L1 (28). In particular, the methionine residue at position 175, which is responsible for hydrophobic intersubunit interactions involved in formation of the L1 dimer, is replaced in THIN-B by a glycine whose side chain lacks any possibility of interacting with the hydrophobic pocket of another subunit. In addition, of the three hydrophobic residues (Leu154, Pro198, Tyr236) that form the L1 hydrophobic pocket where Met175 is accommodated, only Pro198 is conserved in THIN-B (Fig. 2).
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FIG. 2. Amino acid sequence alignment of the THIN-B MBL in comparison with the other subclass B3 enzymes (L1 from S. maltophilia IID1275 [29], FEZ-1 from L. gormanii ATCC 33297 [5], GOB-1 from Chryseobacterium meningosepticum PINT [3], and CAU-1 from Caulobacter crescentus DSM4727 [9]). Residues that are identical in all sequences are boldfaced. The structural elements of L1 are indicated above the sequences ( and 310, helices; ß, strands). Cysteine residues are shaded.
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-helix (15, 28), and which are conserved in THIN-B. The other disulfide bridge would most likely involve residues 208 and 213, which are located at the extremities of the ß11 and ß12 strands, respectively (15). Alternatively, the disulfide bridge could involve the two cysteine residues at positions 32 and 35, which are located close to the N terminus of the protein (Fig. 2). Another notable feature of THIN-B, compared to other enzymes of subclass B3, is its larger protein size (Fig. 2). THIN-B is 29 and 33 amino acids longer, respectively, than L1 and FEZ-1, the two subclass B3 enzymes whose three-dimensional structures have been solved. Sequence comparison and consideration of structural data indicate that most of those extra amino acids are likely to be part of a longer N-terminal coil and of a longer C-terminal ß-helix, with no important modifications of internal elements (Fig. 2).
Kinetic properties of the THIN-B enzyme. Determination of the kinetic parameters of THIN-B with several substrates representative of different ß-lactam families, including penicillins, narrow- to expanded-spectrum cephems, carbapenems, and aztreonam, revealed that all the compounds tested, except aztreonam, were consistently hydrolyzed by the enzyme, although with a remarkable variability of kcat/Km ratios (from 8 x 103 to 5 x 106 M1 · s1) (Table 3). The highest catalytic efficiencies (kcat/Km ratios, >106 M1 · s1) were observed with carbapenems, cefuroxime, and cefotaxime, while cefepime appeared to be a poor substrate. Comparison of Km values indicated a higher apparent affinity for carbapenems and cephalosporins (except cefepime) than for penicillins. The highest turnover rate was observed with ampicillin (kcat, 480 s1), a substrate for which the enzyme also exhibited the highest Km (1.3 mM), resulting in a relatively low catalytic efficiency compared to those of expanded- and broad-spectrum cephalosporins and carbapenems (Table 3). Aztreonam was not hydrolyzed and did not interact with the enzyme (Table 3), as has also been observed with other MBLs (3, 9-13, 20, 22, 23). With cephaloridine (at a substrate concentration of 100 µM), the hydrolysis kinetics presented a notable though slow inactivation pattern until an apparent steady state was reached (rate, 650 µmol/min/mg of enzyme) (Fig. 3). Although the inactivation mechanism has not been further investigated, the most reliable hypothesis possibly explaining a similar behavior could be the existence of two enzyme-substrate complex forms with significantly different turnover rates, leading to accumulation of the enzyme-substrate complex with minor activity. It would be interesting to further investigate this point by mass spectrometry experiments.
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TABLE 3. Kinetic parameters of the purified THIN-B metallo-ß-lactamase and comparison with catalytic efficiencies of other subclass B3 enzymesa
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FIG. 3. Time course for cephaloridine hydrolysis in the presence of 13 nM THIN-B. A steady state was reached after approximately 10 min. Cephaloridine was normally hydrolyzed when 8 nM VIM-2 (10) was added to the reaction mixture, as indicated by the arrow.
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Inactivation of THIN-B by metal chelators. The THIN-B enzyme was efficiently inactivated by EDTA, o-phenanthroline, and dipicolinic acid, allowing the determination of pseudo-first-order inactivation rates (ki).
With EDTA and dipicolinic acid, the inactivation rates varied with the inactivator concentration, following a hyperbolic dependence, and individual inactivation constants (K, k+2, k2') could be calculated (Fig. 4; Table 4). This behavior suggests that the inactivator does not act by simply scavenging the free metal from the buffer but that a ternary enzyme-metal-inactivator complex is formed during inactivation. No similar behavior has been observed for other enzymes of subclass B3 (9, 22), and THIN-B represents the first example of a subclass B3 enzyme for which formation of the ternary complex could be hypothesized.
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FIG. 4. Dependence of the pseudo-first-order inactivation rate (ki) of THIN-B on the concentration of the metal chelator EDTA (a) or dipicolinic acid (b). The line in each graph represents the best fit resulting from the nonlinear regression used to calculate individual inactivation parameters (K, k+2, and k2').
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TABLE 4. Inactivation parameters for the THIN-B metallo-ß-lactamase with various chelating agentsa
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The inactivation efficiencies of chelators were generally high, with values similar to those observed for subclass B1 enzymes (10, 13, 20). Interestingly, with THIN-B, EDTA was a better inactivator than dipicolinic acid or o-phenanthroline (Table 4), at variance from what has generally been observed for MBLs (9, 10, 13, 16, 20, 22).
Concluding remarks. Subclass B3 of MBLs, which until recently included only the L1 enzyme from S. maltophilia, currently includes several members of notable structural and functional diversity. Although produced by a nonpathogenic bacterium, the THIN-B enzyme exhibits some peculiar structural and functional features and could be an interesting model for further structural studies. Moreover, the distribution of MBLs among an increasing number of bacterial species typically associated with environmental niches that might act as a reservoir for efficient resistance determinants might offer an important clue for MBL evolution.
Present address: Laboratoire d'Enzymologie et Centre d'Ingénierie des Protéines, Institut de Chimie, Université de Liège, B-4000 Liège, Belgium. ![]()
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