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Antimicrobial Agents and Chemotherapy, April 2008, p. 1264-1268, Vol. 52, No. 4
0066-4804/08/$08.00+0 doi:10.1128/AAC.00684-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Thierry Lambert,2
Marine Dupêchez,1
Patrice Courvalin,1 and
Marc Galimand1*
Unité des Agents Antibactériens, Institut Pasteur, 75724 Paris Cedex 15,1 Centre d'Etudes Pharmaceutiques, 92296 Châtenay-Malabry, France2
Received 24 May 2007/ Returned for modification 10 August 2007/ Accepted 4 January 2008
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The oxacillin-hydrolyzing β-lactamases (oxacillinases) belong to class D of the Ambler structural classification of β-lactamases (3). These enzymes form a heterogeneous group with respect to their structural and biochemical properties and share a number of unusual features: mainly, they hydrolyze oxacillin more efficiently than benzylpenicillin. In addition, they hydrolyze amoxicillin, methicillin, cephaloridine, and, to some extent, cephalothin, and their activities are usually inhibited by NaCl (13). Only a few variants in Pseudomonas aeruginosa (7, 14) hydrolyze extended-spectrum cephalosporins, and an increasing number are active against carbapenems (20). With a few exceptions, OXA-type β-lactamases are poorly inhibited by clavulanic acid, being classified into group 2d of the functional classification of β-lactamases (3).
Based on their primary structure, class D β-lactamases (DBLs) have three highly conserved active-site elements in common. The first element is the Ser70-Xaa-Xaa-Lys tetrad, where Xaa represents a variable residue, containing the active-site serine (Ser70 according to DBL numbering) (5). The second element, Ser118-Xaa-Val/Ile, is equivalent to the invariable Ser-Asp-Asn motif in class A and the Tyr-Ala/Ser-Asn motif in AmpC β-lactamases, whereas the Lys216-Thr/Ser-Gly element is common to the vast majority of serine-active β-lactamases. Other conserved motifs in DBLs are the Tyr/Phe144-Gly-Asn triad and the Trp232-Xaa-Xaa-Gly tetrad that have no analogues in either class A or AmpC β-lactamases (20).
Although class D enzymes have been reported for a wide variety of bacterial species, such β-lactamases have not yet been described for B. pilosicoli. This report describes the genetic and biochemical properties of a novel molecular DBL, named OXA-63, from the human spirochete B. pilosicoli BM4442.
(An initial report of this work was presented at the 44th Interscience Conference on Antimicrobial Agents and Chemotherapy [6a].)
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Susceptibility testing. Antibiotic susceptibility was tested by disk diffusion on Mueller-Hinton (MH) agar according to standards of the Comité de l'Antibiogramme de la Société Française de Microbiologie (4). MICs of antimicrobial agents for E. coli strains were determined by Etest (AB Biodisk, Combourg, France) on MH agar. For B. pilosicoli, plates containing MH agar supplemented with 5% sheep blood were incubated in an anaerobic jar at 37°C for 3 days.
DNA preparation and transformation. Isolation of total DNA was performed as described previously (17). Restriction with endonucleases was done according to the supplier's recommendations. Amplification of DNA was performed in a 9700 thermal cycler (Perkin-Elmer Cetus, Norwalk, CT) with Taq (Q-BIOgene, Inc., Carlsbad, CA) or Pfu (Stratagene, La Jolla, CA) DNA polymerase as recommended by the manufacturers. PCR elongation times and temperatures were adjusted to the expected size of the PCR product and to the nucleotide sequence of the primers, respectively. The amplification products were purified using the QIAquick PCR purification kit (Qiagen, Inc., Chatsworth, CA). Transformation of E. coli JM83 was performed as described previously (17), with selection on BHI agar containing ampicillin at 50 µg/ml and kanamycin at 40 µg/ml and on chloramphenicol (20 µg/ml) and kanamycin (50 µg/ml) for E. coli BL21(DE3)pLys.
DNA sequence determination and protein analysis. Sequencing of inserts in the recombinant plasmids was performed with a CEQ 2000 DNA analysis system automatic sequencer (Beckman Coulter, Palo Alto, CA). The sequence was analyzed with the GCG sequence analysis software package (version 10.1; Genetics Computer Group, Madison, WI). Blast program searches were performed by using the National Center for Biotechnology Information website (http://www.ncbi.nlm.nih.gov). Multiple sequence alignment of the deduced peptide sequences was carried out using the program ClustalW at the European Bioinformatics Institute website (http://www.ebi.ac.uk./). The SignalP 3.0 server at the ExPASy proteomics server (http://www.expasy.org) was used for the prediction of signal peptide cleavage sites.
Pulsed-field gel electrophoresis and Southern hybridization. A chromosomal location of the oxacillinase gene was investigated in whole-cell DNA of B. pilosicoli BM4442 and 80.10 by the I-CeuI technique (11). After Southern transfer, DNA was hybridized with two 32P-labeled PCR-generated probes: an 807-bp fragment and a 721-bp fragment specific for the blaOXA-63 and 16S rRNA genes, respectively.
Production and purification of OXA-63.
Two deoxyoligonucleotides, oxaF (5'-GGTGGTCTCCCATGTCTAAAAAAAATTTTA-3') and oxaR (5'-CTCCTCGAGTTTTAATAAATTTAATGCTTT-3'), containing BsaI and XhoI restriction sites (underlined), were used to amplify the blaOXA-63 gene from pAT784 with Pfu polymerase. The PCR product was cloned in the pCR-Blunt vector, resequenced, and subcloned under the control of the T7 promoter in pET28a(+) previously digested with NcoI and XhoI enzymes, producing pAT852 [pET28a(+)
blaOXA-63].
The OXA-63 enzyme engineered to have a C-terminal His6 tag enzyme was purified from E. coli BL21(DE3)pLys harboring plasmid pET28a(+)
blaOXA-63 as follows. The strain was grown in 0.5 liters of BHI broth containing kanamycin (50 µg/ml) and chloramphenicol (20 µg/ml) at 37°C to an optical density at 600 nm of 1.0, at which point isopropyl-1-thio-β-D-galactopyranoside was added to a final concentration of 0.5 mM. After 4 h of induction at 28°C, the cells were harvested by centrifugation and used immediately or stored at 80°C. The cell pellet was resuspended (4 ml/g of wet cells) in buffer A (20 mM sodium phosphate [pH 7.4] containing 0.5 M NaCl and 20 mM imidazole) and disrupted by sonication (five times for 30 s each time at 60 W). Cellular debris was removed by centrifugation (15,000 x g for 1 h at 4°C), and the supernatant was collected, filtered (0.22 µm), and applied to a HisTrap Fast Flow column (1 ml, 1.0-ml/min flow rate; GE Healthcare, Uppsala, Sweden) previously equilibrated with buffer A. The enzyme was eluted with a linear gradient of 20 to 500 mM imidazole over 30 ml. Fractions (1 ml each) containing the recombinant OXA-63 were analyzed for purity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and the pure fractions were pooled, dialyzed against 20 mM sodium phosphate-0.15 M NaCl (pH 7.4), and concentrated to 1 mg/ml with a Centriprep 30 concentrator (Amicon). Protein purity was estimated by SDS-PAGE analysis. The enzyme concentration was determined on the basis of A280 assuming an
of 35410 cm–1 M–1 as calculated by ProtParam of the ExPASy proteomics server. The purified enzyme (1 mg/ml) was stored at 4°C.
NH2-terminal sequencing of OXA-63. The presence of a putative signal peptide cleavage site was investigated by N-terminal Edman sequencing on an Applied Biosystems Procise sequencer with the reagents and methods recommended by the manufacturer.
Determination of kinetic parameters of OXA-63. Purified OXA-63 was used for the determination of kinetic parameters (kcat and Km), which was performed at 25°C in 100 mM sodium phosphate (pH 7.0) in a total volume of 0.5 ml. The initial rates of hydrolysis were determined with a Uvikon UV931 spectrophotometer (Kontron Instruments). The wavelengths and changes in extinction coefficients of β-lactams were previously described (16). The enzyme concentration in the reaction mixture was in the range of 50 to 150 nM. The steady-state kinetic parameters were determined using the Hanes-Woolf plot (8). The 50% inhibitory concentration (IC50) was determined as the β-lactamase inhibitor or NaCl concentrations that reduced the hydrolysis rate of 100 µM nitrocefin by 50% when the enzyme was preincubated with various concentrations of inhibitor for 30 min at 25°C before the addition of the substrate (14).
Size-exclusion chromatography. Size-exclusion chromatography was performed using a Hiload 16/60 Superdex 75 column (GE Healthcare) equilibrated with 50 mM sodium phosphate buffer containing 0.15 M NaCl (pH 7.0) and eluted in the same buffer at a flow rate of 1 ml/min. The column was calibrated using aprotinin (Mr, 6,500), RNase A (Mr, 13,700), carbonic anhydrase (Mr, 29,000), and conalbumin (Mr, 75,000).
Nucleotide sequence accession number. The nucleotide sequence of the blaOXA-63 gene and of the flanking regions has been deposited in the GenBank database under accession number AY619003.
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TABLE 1. MICs of β-lactams for B. pilosicoli and E. coli strains with or without OXA-63
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Comparison of the sequence of the insert of pAT784 with sequences in the GenBank database revealed 70% identity over 620 nucleotides to the blaFUS-1 gene belonging to DBLs (EMBL/GenBank accession number AY227054), and the gene was named blaOXA-63. A putative ribosome binding site, AAGGA, was located 6 bp upstream from an ATG initiation codon leading to a sequence of 807 bp. Analysis of the upstream sequence indicated the presence of a putative promoter composed of –35 TTGACA and –10 TATACT motifs separated by 17 bp (Fig. 1).
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FIG. 1. Deduced sequence of OXA-63 aligned with the corresponding gene. The –35 (TTGACA) and –10 (TATACT) regions and the ribosome binding site (RBS) are indicated in boldface type. The motifs usually conserved among DBLs are double underlined, and their location is indicated according to the DBL numbering system (5). The star indicates the stop codon.
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Structural properties of OXA-63. OXA-63 exhibited the three highly conserved active-site elements of DBLs. The first one, the Ser-Thr-Phe-Lys tetrad containing the active-site serine, was found at positions 70 to 73 (Ser70 according to DBL numbering) (5); the second element, Ser-Gln-Val, was at DBL 118 to 120; and the third, Lys-Thr-Gly, was at positions 216 to 218. The Tyr-Gly-Asn triad (DBL positions 144 to 146) found in oxacillinases was replaced by the Phe-Gly-Asn motif as in most carbapenem-hydrolyzing oxacillinases, and the Trp-Phe-Val-Gly tetrad was at positions 232 to 235 (Fig. 1).
OXA-63 had 25 to 44% identity with various DBLs and shared 53% identity with FUS-1 (OXA-85), a recently described oxacillinase from the anaerobic gram-negative rod Fusobacterium nucleatum subsp. polymorphum (19). Phylogenetic analysis indicated that OXA-63 exhibited the closest ancestral relationship with putative products from the genomes of Campylobacter jejuni (OXA-61) (1) and Campylobacter lari RM2100 (GenBank accession no. ZP_00369367) and clustered with a group of chromosomally encoded enzymes including OXA-50 (7) and some homologues detected in the genomes of various bacterial species such as Thiomicrospira denitrificans ATCC 33889 (accession no. YP_393464) and Methylobacillus flagellatus KT (accession no. ZP_00564423).
Purification and characterization of the OXA-63 β-lactamase.
The carboxy-terminal His6-tagged OXA-63 was expressed in E. coli BL21(DE3)pLys harboring plasmid pAT852 [pET28a(+)
blaOXA-63]. The weak rate of expression (ca. 5% of total proteins) was possibly due to the low G+C content (25%) of the blaOXA-63 gene. OXA-63 was purified from the crude lysate by single-step nickel affinity chromatography. The protein was >95% pure, as judged by SDS-PAGE analysis (data not shown). Overall, the procedure yielded approximately 2 mg of purified OXA-63 per liter of culture. The Mr of the native protein determined by size-exclusion chromatography was estimated to be 63 kDa, suggesting that the native protein is a dimer.
The SignalP 3.0 server suggested that OXA-63 could be a nonsecreted protein. This was confirmed by the N-terminal amino acid sequencing of the mature protein, which did not reveal a cleavage site. The SKKNFI sequence obtained corresponded to that of the native protein without the methionine. Moreover, study of the location of OXA-63 in E. coli by Western blotting indicated that the majority of the enzyme was present in the membrane fraction, with only small amounts in the cytoplasmic and periplasmic fractions. These data suggest that OXA-63 could be the first example of a membrane-located β-lactamase in gram-negative bacteria.
Kinetic parameters indicated that the OXA-63 β-lactamase has a narrow substrate profile that includes benzylpenicillin, oxacillin, and ampicillin (Table 2). Oxacillin was the best substrate, with a high turnover rate (kcat, 113 s–1) and consequently a high catalytic efficiency (kcat/Km, 9.8 x 105 M–1 s–1), being hydrolyzed four- and sixfold more efficiently than benzylpenicillin and ampicillin, respectively. Despite the high affinity (low Km values) of OXA-63 for ampicillin, benzylpenicillin, piperacillin, and carbenicillin, the turnover rates were low (kcat of <10 s–1). Even at high concentrations (1 µM), OXA-63 did not hydrolyze cefotaxime, ceftazidime, cefepime, imipenem, and aztreonam. Interestingly, OXA-63 had no carbapenem-hydrolyzing activity, although it had the Phe-Gly-Asn triad present in most carbapenem-hydrolyzing oxacillinases. This is in agreement with mutagenesis studies showing that the Phe residue at DBL position 144 is not, by itself, responsible for carbapenem-hydrolyzing activity (9, 15). No biphasic kinetic was observed for all the substrates tested.
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TABLE 2. Kinetic parameters of purified OXA-63 β-lactamase for hydrolysis of some β-lactams in comparison with FUS-1a
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In contrast with FUS-1 and other DBLs, OXA-63 was strongly inhibited by clavulanate (IC50, 2 µM), tazobactam (IC50, 0.16 µM), and sulbactam (IC50, 12 µM). These data are in agreement with the susceptibility patterns of B. pilosicoli BM4442 and E. coli JM83 carrying the cloned blaOXA-63 gene. The strains were resistant to most penicillins, whose antimicrobial activities were restored by clavulanic acid and tazobactam (Table 1). OXA-63 was poorly inhibited by NaCl (IC50, >2 M), which represents an important difference from other oxacillinases that are usually inhibited by chloride ions (IC50, 250 mM) (13). Resistance to inhibition and, conversely, susceptibility to inhibition by NaCl are related to the presence of Phe and Tyr, respectively, at DBL position 144 (13, 15). OXA-63 was resistant to NaCl (IC50, >2 M), suggesting that the Phe144 residue may prevent NaCl from affecting the active site.
In conclusion, this work characterizes the genetics and biochemistry of the new narrow-spectrum OXA-63 DBL from B. pilosicoli BM4442.
We thank P. E. Reynolds for reading of the manuscript.
Published ahead of print on 22 January 2008. ![]()
Present address: Laboratoire de Biochimie Appliquée, Faculté des Sciences, Université Ferhat Abbas, 19000 Sétif, Algeria. ![]()
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