INTRODUCTION

The vancomycin class of glycopeptide antibiotics binds with high affinity to the N-acylated D-Ala-D-Ala termini of intermediates in assembly and cross-linking of peptidoglycan (PG)¹ strands in bacterial cell wall biosynthesis (1-4) at the external face of the cell membrane. The vancomycin·PG·D-Ala-D-Ala complex is blocked for subsequent transpeptidations and transglycosylations, by which new chains are added and existing PG chains are cross-linked. The net reduction in covalent connectivity of PG translates into reduced tensile strength and increased susceptibility to osmotic lysis and bacterial death.

Clinically significant vancomycin resistance has been detected in pathogenic enterococci in three phenotypic forms, designated VanA, VanB, and VanC type resistance (2). The VanA phenotype has been best studied and found to require the expression of five genes where all five encoded proteins VanR, -S, -H, -A, -X have enzymatic activities (2, 4). VanS and -R act as partners in a two-component regulatory system, VanS as a transmembrane sensor kinase (5, 6) and VanR as a response regulator (6, 7), which account for inducible transcriptional activation of VanH, -A, and -X. VanH encodes a D-Lac dehydrogenase, functioning as a D-specific pyruvate reductase (8) to provide D-Lac for VanA, which is a D-Ala-D-Ala ligase homolog that has gained D-Ala-D-Lac depsipeptide ligase activity (8, 9). In a cell producing both D-Ala-D-Ala and D-Ala-D-Lac (Scheme 1, a and b), VanX acts selectively as a D-Ala-D-Ala dipeptidase. Thus, D-Ala-D-Lac accumulates (10) and serves as a substrate for the MurF enzyme that normally adds D-Ala-D-Ala as a unit to a UDP-N-acetylmuramic acid (MurNAc) tripeptide. Instead of the normal UDP-MurNAc pentapeptide terminating in D-Ala-D-Ala, a UDP-MurNAc tetrapeptide ester terminating in D-Ala-D-Lac is produced in such a vancomycin-resistant Enterococcus sp. Vancomycin binds with three orders of magnitude lower affinity to the D-Ala-D-Lac terminus versus the D-Ala-D-Ala terminus, accounting quantitatively for observed resistance levels (8).

Scheme 1.

The molecular analysis of vancomycin resistance has led to the similarities and differences between the dipeptide forming D-Ala-D-Ala ligases and the ~28% identical 38 kDa D-Ala-D-Ala ligase homolog VanA, whose gain of depsipeptide ligase activity is crucial for phenotypic resistance (8, 9). The x-ray structure of the DdlB isoform of Escherichia coli in complex with a phosphinophosphate analog of a dipeptidyl reaction intermediate has allowed definition of the ligase active site (11) and predicted functions for several residues that were validated by mutagenesis (12). Most intriguingly, mutations at Tyr²¹⁶ (Y216F) or Ser¹⁵⁰ (S150A) in the E. coli DdlB convert the dipeptide ligase to an enzyme that has now gained substantial depsipeptide ligase activity (13) that is the hallmark of a VanA and -B type dipeptide/depsipeptide ligase. An x-ray structure of E. coli Y216F DdlB has been obtained (14). Both Tyr²¹⁶, on a mobile omega-loop, and Ser¹⁵⁰ participate, with Glu¹⁵, in wild-type E. coli DdlB in a hydrogen bonding array that fixes the omega-loop to cover the substrates and intermediates in the active site and to hydrogen bond (Glu¹⁵) to the amino group of D-Ala₁ to orient this electrophilic substrate (Fig. 1). It was this hydrogen bonding array that suggested Tyr²¹⁶ as a potentially important residue.

In addition to studying the vanR, -S, -H, -A, and -X operon function, the structure of PG intermediates in Gram-positive bacteria with intrinsic vancomycin resistance such as Lactobacillus, Pediococcus, and Leuconostoc species has been analyzed (16-19). In these cases, PG intermediates terminating in D-Ala-D-Lac were also detected (20, 21), suggesting a common evolutionary mechanism and a possible origin for at least the VanH and -A genes. Polymerase chain reaction (PCR) analysis has been used to identify and sequence fragments of the ddl genes in such organisms (22), and there is a correlation of Tyr/Phe in the D-Ala-D-Ala ligases at the position corresponding to Tyr²¹⁶ in E. coli DdlB with sensitivity/resistance phenotypes (13). To test the prediction that a phenylalanine in the omega-loop region does indeed predict a D-Ala-D-Ala ligase with depsipeptide ligase activity, D-Ala-D-Ala ligase from vancomycin-resistant Leuconostoc mesenteroides ATCC 8293 was overproduced, purified from E. coli extract, and characterized for D-Ala-D-Ala and D-Ala-D-Lac ligase activities. When Phe²⁶¹ was then mutated to Tyr, the resultant enzyme shows retention of D-Ala-D-Ala dipeptide ligase activity but loss of D-Ala-D-Lac depsipeptide ligase activity.

EXPERIMENTAL PROCEDURES

L. mesenteroides ATCC 8293 was from American type culture collection (ATCC). Oligonucleotides were purchased from Integrated DNA Technologies, Inc (Coralville, IA), and restriction enzymes and polymerases were from U. S. Biochemical, Corp. (Cleveland, OH). ATP, D-Ala, DL--hydroxybutyrate (Hbut), D-Lac, phosphoenolpyruvate, and HEPES were purchased from Sigma. NADH, L-Lac dehydrogenase, and pyruvate kinase were from Boehringer Mannheim. D-[¹⁴C]-Ala and D-[¹⁴C]-Lac were from American Radiolabeled Chemicals Inc. (St. Louis, MO), and thin layer chromatography (TLC) cellulose sheets were from Kodak (Rochester, NY).

Cloning was carried out by amplification of a DNA fragment by using two rounds of PCR of genomic DNA purified from L. mesenteroides ATCC 8293. Three PCR oligonucleotides (oligomer 1, CATAC AAGGT GAGGA CGGAA AGATG; oligomer 2, GCGGA TCCTT AGTTA AACTT CCCTA TCTTT TCTTC TCCAA GTGAC; and oligomer 3, GCACA TTCTA GAAGG AGACG GACAT ATGAC TAAAA AAAGA GTAGC) used in this reaction were designed on the basis of the published L. mesenteroides CIP 16407 sequences (22). The first round of PCR with oligomers 1 and 2 was for the amplification of the corresponding genomic DNA fragment. Oligomer 1 was designed to hybridize to the upstream region of the lmddl gene, and oligomer 2 contains the 3 terminal 37 bases of the gene and additional sequences to introduce a BamHI restriction site. Three separate clonings resulted in the same DNA sequence. In the sequence, some variations were detected, as noted below, compared with the sequence previously reported for a different subtype (ATCC 8293 versus CIP 16407, see Ref. 22). Therefore, this gene is designated lmddl2. The differences in the DNA sequences and their corresponding effects on the encoded peptide sequence (CIP versus ATCC strains) are Ala¹³⁰ to Gly (Asp³⁵ to Gly), Thr²³⁶ to Cys (silent), Ala²⁵⁸ Gly²⁵⁹ to Gly-Cys (Ser⁷⁸ to Ala), Gly³¹⁷ to Cys (Leu⁹⁷ to Phe), and Cys⁶⁸⁶ to Thr (silent), resulting in three amino acid changes between LmDdl and LmDdl2. The subsequent round of PCR where the above PCR product was template with oligomers 2 and 3, was performed to produce an XbaI restriction enzyme site and Shine-Dalgano sequences at the upstream site of the gene as described earlier (23). The DNA fragment was subcloned into the XbaI-BamHI site of pET22b (Novagen, Madison, WI) and transformed into E. coli DH5 and subsequently into E. coli BL21(DE3). Site-directed mutagenesis at the Phe²⁶¹ site was carried out by using two-round megaprimer PCR (24). The oligonucleotides used were the above two oligmers 2 and 3 and a mutated sequence oligomer (GGAAT TATCA ACGTA CTTAT TATTA TAATC ATACC). After mutagenesis the sequences were confimed by DNA sequencing.

Cell culture and purification of DdlB, Y216F, and VanA were performed as described previously (12). Those of wild type and F261Y LmDdl2 are essentially the same as the above proteins with minor modifications. Briefly, Luria-Bertani medium was inoculated by 1/40 volume of the overnight culture of the corresponding strain and incubated at 30 °C to A₅₉₅ 0.6. At this time, 0.4 mM (final concentration) isopropyl-thio--D-galactoside was added to induce lmddl2 gene expression, and the culture was further incubated for ~3 h. The harvested cells in buffer P containing 50 mM Hepes buffer, pH 7.2, and 10 mM MgCl₂ were disrupted by French press (18,000 psi/in²), and the supernatant was obtained after 30 min of centrifugation of the resulting cell extract at 100,000 × g. Most of the LmDdl2 protein was recovered in the supernatant. Purification of the protein was followed by ammonium sulfate fractionation (25~50% fraction), ACA54 gel (BioSepra, Marlborough, MA) filtration, and Q-Sepharose chromatography (column size, 80 ml; elution, 400 ml of buffer P; gradient, 0-1 M KCl). In the gel filtration chromatography, the LmDdl2 protein (~42 kDa) was recovered in similar fractions as DdlB, which is a dimer of a 32 kDa polypeptide. Thus, LmDdl2 also appears to be a dimer. The purities of both wild-type and F216Y mutant proteins were measured to be around 90% by gel scanning densitometry of an SDS gel.

The assay mixture included 0.2 mM D-[1-¹⁴C]-Ala (0.1 mCi/ml, 55 µCi/µmol) or 0.2 mM D-[1-¹⁴C]-Lac (0.1 mCi/ml, 55 µCi/µmol), 100 mM HEPES, pH 7.5, 10 mM KCl, 10 mM MgCl₂, 10 mM ATP, and additional unlabeled D-Ala, D-Lac, or DL-Hbut with enzyme (~10 µM), which was incubated at room temperature for 3 h. Three µl of each sample was analyzed on TLC cellulose plate as described previously (8, 9).

The TLC assay was not suitable for measurement of kinetic parameters of LmDdl2 because it was necessary to incubate the reaction mixture for more than 30 min to detect any turnover, and it was difficult to find the linear region of enzyme activity. For these reasons, the ADP release-coupled assay (25) was routinely used for evaluating kinetic parameters. The reaction mixture was composed of 100 mM HEPES, pH 7.5, 10 mM KCl, 10 mM MgCl₂, 10 mM ATP, 2.5 mM phosphoenolpyruvate, 0.15-0.2 mM NADH, 50 units/ml L-Lac dehydrogenase, 50 units/ml pyruvate kinase, D-Ala and D-Lac. The assay was initiated by adding enzymes at 30 °C, and reaction progress was monitored at 340 nm.

The kinetic analysis was carried out as described previously (13, 26-29). The basic equation for D-Ala-D-Ala ligase (Equation 2) was derived based on the steady-state kinetics for two identical substrate molecules of D-Ala (Equation 1).

(Eq. 1)

(Eq. 2)

For several different conditions of [S]K_m1, K_m1[S]K_m2, K_m1[S] (< or  K_m2) or K_m2[S], Equation 2 can be approximated by Equations 3, 4, 5, or 7, respectively.

(Eq. 3)

(Eq. 4)

(Eq. 5)

(Eq. 6)

Because of lack of saturation by D-Ala as shown in Fig. 4, it was not possible to measure V_max and K_m2 values for the D-Ala-D-Ala ligase activity of LmDdl2 wild-type and F261Y mutant proteins. According to the above approximations, it is apparent that in Fig. 4, the concentrations of D-Ala vary from around K_m1 to much less than K_m2. k_cat/K_m2 values were therefore obtained by measuring the slope values of the linear portions of reaction time courses.

D-Ala-D-Lac ligase activities were measured as described previously (13). Briefly, Equation 8 was used based on Equation 7, where S₁ and S₂ are D-Ala and D-Lac, respectively. Those activities were measured by the ADP release-coupled assay. Because this method cannot discriminate D-Ala-D-Lac ligase activity from D-Ala-D-Ala ligase activity (paths a and b in Scheme 1), the velocity values were corrected. The value obtained from the observed activity minus D-Ala-D-Ala ligase activity in the absence of D-Lac was regarded as D-Ala-D-Lac ligase activity because, in the conditions used (for D-Ala-D-Lac ligase activity of LmDdl2 wild-type), the D-Ala-D-Ala ligase activity is less than 5% of the maximum observed activity.

(Eq. 7)

(Eq. 8)

For the D-Ala-D-Lac ligase activity of LmDdl2 wild-type and F216Y mutant proteins, D-Ala was included at the indicated concentration. To calculate the true K_m2 value for D-Lac, it is necessary to know the first K_m1 value for D-Ala. However, because of the kinetic complexity, K_m1 for D-Ala₁ could not be determined. Thus, the K_m2 and k_cat/K_m2 value for LmDdl2 wild-type D-Ala-D-Lac ligase activity in Table I are apparent values.

Table I. Kinetic parameters of LmDdl2, DdlB and VanA proteinsa Protein Activity Km1b Km2c kcat kcat/Km2      Km (ATP) mM mM min1 mM1 min1 mM LmDdl2 Wt A-Ad NDe  150f NDe 0.35 3 0.71g A-Lh NDe 20i 23 1.2i LmDdl2 F261Y A-Ad 14 130 140 1.1 0.49g DdlB A-Ad 0.003 2 880 440 0.049 DdlB Y216F A-Ad 0.33 16 630 39 0.04 0.033 A-Lh NDe 27 42 1.6 VanA Wt A-Ad 0.1  100f 940 1.7 30 0.116 A-Lh 0.23 0.88 45 51 a Measured by ADP coupled assay. b Km for D-Ala1. c Km for D-Ala2 or D-Lac at subsite 2. d D-Ala-D-Ala ligase. e ND, not determined. f The highest concentrations of D-Ala used. g Apparent values determined with 100 mM D-Ala. h D-Ala-D-Lac ligase. i Apparent values determined with 10 mM D-Ala.

RESULTS

The gene encoding the putative D-Ala-D-Ala ligase from the vancomycin-resistant L. mesenteroides ATCC 8293 (reported MIC 1012 µg/ml) (20, 21) was subcloned into plasmid pET22b behind the T7 promoter as noted under "Experimental Procedures," expressed in E. coli BL21(DE3), and purified as summarized in Fig. 2. Overproduction of the ~42 kDa LmDdl2 was obtained in soluble form and was readily purified by gel filtration and ion exchange chromatography. A yield of 30 mg of enzyme from ~5 g (wet weight) of E. coli was obtained. Fig. 3A shows the profile of products from pure LmDdl2 by TLC analysis in which radiolabeled D-[¹⁴C]-Ala was the tracer substrate and D-[¹⁴C]-Ala-D-[¹⁴C]-Ala and D-[¹⁴C]-Ala-D-Hbut products were detected. D-Hbut was utilized as a surrogate substrate for D-Lac in these assays as in earlier studies (8, 9, 13) since D-Ala-D-Lac comigrates with D-Ala-D-Ala on TLC while D-Ala-D-Hbut depsipeptide migrates with higher mobility. The enzyme LmDdl2 makes D-[¹⁴C]-Ala-D-Hbut as does VanA and, albeit more slowly, E. coli Y216F DdlB, shown as positive controls for depsipeptide ligase activity, whereas wild-type E. coli DdlB makes only dipeptide. In Fig. 3B, cognate incubations with D-[¹⁴C]-Lac as tracer show the depsipeptide ligase capacity with D-Lac as a nucleophilic hydroxy acid cosubstrate for LmDdl2.

Table I summarizes steady-state kinetic data for LmDdl2 for D-Ala₁, D-Ala₂, and D-Lac, using a continuous coupled assay for ADP production as previously reported (25). The affinity for D-Ala₁ and D-Ala₂ could not be readily determined in contrast to several of the other enzyme forms in the table. It is clear that K_m2 for D-Ala₂ is very high and most probably non-physiological. The k_cat values for D-Ala-D-Lac ligase activity of LmDdl2 (23 min¹) and of the E. coli Y216F DdlB mutant (42 min¹) approximate those previously reported for VanA (45 min¹) (13). Typically, these k_cat values are less than those for D-Ala-D-Ala dipeptide synthesis, perhaps reflecting the weaker nucleophilicity of D-Lac versus D-Ala₂ in capturing the D-Ala₁-PO₃ intermediate. The best determined steady-state parameter for wild-type LmDdl2 was k_cat/K_m2 of 0.35 min¹ mM¹ for D-Ala₂ as the nucleophile cosubstrate and 1.2 for D-Lac as the nucleophile substrate for a catalytic efficiency ratio of ~3/1 in favor of depsipeptide. By comparison, the corresponding (k_cat/K_D-Lac)/(k_cat/K_D-Ala2) for VanA is ~30/1. The E. coli DdlB Y216F mutant that has gained D-Ala-D-Lac depsipeptide ligase activity has a corresponding ratio of 0.04. Thus, the LmDdl2 is intermediate in its preferential catalytic efficiency to make D-Ala-D-Lac instead of D-Ala-D-Ala. Given the vancomycin resistance phenotype and the exclusive detection of D-Ala-D-Lac termini in UDP-MurNAc peptide intermediate (20, 21), it may be that LmDdl2 functions in depsipeptide ligase mode in vivo.

In the LmDdl2 F261Y mutant (see below) in which no residual activity to synthesize D-Ala-D-Lac is detectable, the k_cat/K_D-Ala2 value has increased three-fold (to 1.1 mM¹ min¹), as shown by the data of Fig. 4C.

To test the proposition that Phe²⁶¹ in LmDdl2, analogous to the Y216F mutant of E. coli DdlB (13), is involved in the gain of function depsipeptide ligase activity of wild-type LmDdl2, the LmDdl2 F261Y mutant was constructed, and the enzyme was purified (to ~90% homogeneity) with the prediction that it should retain dipeptide ligase activity but be selectively ablated for depsipeptide ligase activity. This enzyme has the activity shown in Fig. 4B as a function of added D-Lac. While wild-type LmDdl2 (Phe²⁶¹) has both D-Ala-D-Ala ligase activity and D-Ala-D-Lac ligase activity, the F261Y enzyme has no detectable ability to utilize D-Lac (at up to 100 mM concentration) either at 3 or 10 mM concentrations of cosubstrate D-Ala. Wild-type LmDdl2 saturates at about 50 mM D-Lac. While the F261Y LmDdl2 is inactive with D-Lac, it actually has a more robust D-Ala-D-Ala ligase activity (Fig. 3C).

DISCUSSION

This work describes the purification and initial kinetic characterization of a D-Ala-D-Ala ligase for the first time from a Gram-positive bacterium, L. mesenteroides, known to possess intrinsic chromosomally mediated resistance to the antibiotic vancomycin (20, 21). As previously demonstrated for the enterococcal VanA enzyme (8, 9), LmDdl2 does indeed possess both dipeptide ligase (D-Ala-D-Ala) and depsipeptide ligase activity (D-Ala-D-Lac, D-Ala-D-Hbut), consistent with both the vancomycin-resistance phenotype and the detection of cell wall PG intermediates terminating in D-Ala-D-Lac² (20, 21). These activities pinpoint this chromosomal D-Ala-D-Ala ligase as a key molecular determinant in the antibiotic resistance phenotype. The gain of depsipeptide ligase activity of LmDdl2 generalizes previous observations on VanA and VanB-containing drug-resistant enterococci to the naturally resistant Gram-positive soil bacterium and increases the probability that this will be the immunity mechanism for vancomycin producing steptomyces.

It has been noted that a striking correlation exists for the occurrence of Tyr/Phe at position 216 with the vancomycin sensitivity/resistance phenotype (13). In the comparison of the Tyr²¹⁶ or equivalent residue (Fig. 5), it is conceivable that there are three classes. The first class, with Tyr in that position, includes 11 proteins. Among them, eight proteins are known or proposed to be D-Ala-D-Ala ligases (8, 9, 25, 29), whereas VanC1, 2, 3 were predicted to be D-Ala-D-Ser ligases since D-Ala-D-Ser terminating UDP-MurNAc was detected in enterococci containing these proteins (37). The lower affinity for D-Ala-D-Ser (amide) versus D-Ala-D-Ala (amide) is ascribed to steric clash of the hydroxymethyl side chain of D-Ser in the complex with vancomycin.

The second group includes four proteins from Gram-positive bacteria (Lc, Lm, Lp, Ls D-Ala-D-Ala ligases in Fig. 5) that contain Phe instead of Tyr. The Tyr/Phe7 replacement has previously been tested in one direction, by converting wild-type E. coli DdlB to the Y216F mutant (13). As summarized in Table II, this results in specific gain of function of depsipeptide ligase activity. Wild-type LmDdl2 with the Phe residue similarly has D-Ala-D-Lac ligase activity. The reverse mutation F261Y yields mutant LmDdl2 that retains an increasingly efficient D-Ala-D-Ala ligase but, indeed, has lost all detectable depsipeptide ligase activity. X-ray structures are available for wild-type E. coli DdlB (11) and now for the E. coli Y216F DdlB (14), but the altered ability to activate D-Lac C₂-OH as a nucleophile is not yet clear. Crystal structures for the wild-type and mutant pair of LmDdls may also be needed to decipher the amine versus hydroxyl specificity in D-Ala₂ versus D-Lac.

Table II. Summary of results Organism Enzyme Residue Depsipeptide Dipeptide E. coli DdlB wild-type Tyr   + DdlB Y216F mutant Phe + + L. mesenteroides LmDdl2 wild-type Phe + + LmDdl2 F261Y mutant Tyr   +

In VanA and B isoforms, which may comprise the third group, the homology suggests a slightly altered loop region and no obviously discernible aromatic residue that is isofunctional to Phe²¹⁶ or Phe²⁶¹ of E. coli DdlB or LmDdls. This may indicate a microscopically different structural solution for a loop in VanA and VanB, permitting D-Lac to function as a nucleophilic cosubstrate. D-Ala-D-Lac has 800-1000-fold lower affinity for vancomycin compared with D-Ala-D-Ala because of the ester for amide substitution (8, 9).