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Journal of Bacteriology, June 2007, p. 3954-3959, Vol. 189, No. 11
0021-9193/07/$08.00+0 doi:10.1128/JB.00262-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Department of Biology, Georgia State University, Atlanta, Georgia 30303
Received 15 February 2007/ Accepted 26 March 2007
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1-piperideine-2-carboxylate as its transamination product. These results implied that AruH may have a broader physiological function in amino acid catabolism. |
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Synthesis of 2-ketoarginine from L-arginine can also be accomplished by the transamination reaction (14). In the accompanying paper (17), we reported an arginine-inducible arginine transaminase (ATA) activity in P. aeruginosa PAO1, and this activity was completely abolished when the aruH gene was deleted. The aruH gene was proposed to encode a putative ATA residing in a multigene operon that is highly conserved in P. aeruginosa, P. putida, and Pseudomonas fluorescens (17).
In the present study, we purified the His-tagged AruH protein from Escherichia coli and characterized its enzymatic properties. Evidence is provided herein that AruH indeed catalyzes a transamination reaction with pyruvate as the amino acceptor, following a ping-pong bi-bi kinetics model. When L-arginine was used as the amino donor, the products of this transamination reaction, 2-ketoarginine and L-alanine, were confirmed by high-performance liquid chromatography (HPLC) and mass spectrometry (MS) and the kinetic properties were analyzed by a coupled reaction with NAD+ and L-alanine dehydrogenase.
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Purification of His6-tagged AruH. Recombinant AruH was purified using a HisTrap HP kit (GE Healthcare) according to the manufacturer's instructions. Briefly, the cell pellet (approximately 10 g) was suspended in 20 ml phosphate buffer (20 mM sodium phosphate, 500 mM NaCl, 20 mM imidazole, pH 7.4). EDTA-free protease inhibitor cocktail (two tablets; Roche) was added, and the cells were ruptured by an Aminco French pressure cell at 8,000 lb/in2. Cell debris was removed by centrifugation at 25,000 x g for 30 min, and the resulting cell-free crude extract was applied to a HisTrap HP column (GE Healthcare) equilibrated with the sodium phosphate buffer described above. After washing away of the unbound proteins with equilibration buffer, His-tagged AruH was eluted with a stepwise gradient of 150 mM imidazole in 20 mM phosphate (pH 7.4) and 500 mM NaCl. For further purification, AruH proteins were subjected to anion-exchange chromatography using a Mono Q HR 5/5 column (Pharmacia) equilibrated with 20 mM Tris/HCl (pH 7.4; buffer A). A protein sample was applied to the column and eluted with buffer A, followed by a linear gradient of 0 to 1 M KCl in buffer A over 20 column volumes. Active fractions that were homogeneous, as determined by visual inspection of sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis gels, were pooled and then desalted and concentrated using an Aminco Ultra-15 centrifugal filter unit (molecular mass cutoff, 30 kDa; Millipore). UV-visible light absorption spectra of the purified protein (8 mg/ml) in buffer A were recorded at 25°C with a Cary 3E spectrophotometer (Varian). Aliquots of AruH, supplemented with 50 µM pyridoxal 5'-phosphate (PLP) and EDTA-free protease inhibitor cocktail, were stored at 4°C before use for enzyme assays (up to 1 week of storage).
Gel filtration analysis. Gel filtration was performed with low- and high-molecular-weight calibration kits (GE Healthcare) by using a Superdex 200 HR 10/30 column (GE Healthcare) equilibrated with 50 mM sodium phosphate (pH 7.4) containing 300 mM NaCl. Recombinant AruH (50 µl; 5 mg/ml) was injected into the column and eluted at a flow rate of 0.5 ml/min. The molecular mass standards used were thyroglobulin (669 kDa), catalase (232 kDa), aldolase (158 kDa), bovine serum albumin (67 kDa), ovalbumin (43 kDa), and chymotrypsinogen A (25 kDa).
Identification of 2-ketoarginine as a product of the AruH reaction by HPLC. A reaction mixture (1.0 ml) containing 10 µg of recombinant AruH, 20 mM L-arginine, 20 mM pyruvate, and 0.5 mM PLP in 70 mM Tris/HCl buffer (pH 9.0) was incubated for 1 h at 37°C. After incubation, the sample was boiled for 10 min and then filtered using an Ultrafree-0.5 PBCC centrifugal filter unit (molecular mass cutoff, 5 kDa; Millipore). In a negative control experiment, heat-denatured recombinant AruH was used to prepare the reaction mixture. Reaction samples were separated on a Breeze HPLC system (Waters) equipped with a Develosil RP-Aqueous C30 column (4.6 by 250 mm; Phenomenex) at a flow rate of 1 ml/min. The mobile phase was 0.1 M potassium phosphate (pH 2.0), and elution was monitored by UV detection at 205 nm. Authentic L-arginine, pyruvate, PLP, and 2-ketoarginine were used as standards. A protocol described by Jann et al. (6) was followed to prepare 2-ketoarginine.
For the reversible reaction, 2-ketoarginine and L-alanine at 20 mM were used as substrates to replace 20 mM L-arginine and pyruvate under the assay conditions described above, followed by HPLC analysis.
MS of AruH reaction products. Samples prepared as described above for HPLC analysis were submitted for electrospray ionization (ESI)-MS analysis at the MS facility of Georgia State University. In the L-lysine experiments, 20 mM L-lysine was used to replace 20 mM L-arginine as the amino donor. The samples were diluted with methanol (1:1, vol/vol) and introduced into a Q-Tof micro MS apparatus (Waters) for analysis using the negative mode by infusion injection at a flow rate of 5 µl/min, with a capillary voltage of 3.5 kV, a sample cone voltage of 25 V, and an extract cone voltage of 1.0 V.
Enzyme assays.
The arginine:pyruvate transaminase activity of recombinant AruH was measured in two steps. The first step was a transamination reaction catalyzed by recombinant AruH, in which the
-amino group of L-arginine was transferred to pyruvate, making 2-ketoarginine and L-alanine. In the second step, the amounts of L-alanine formed in the transamination reaction were determined by an enzyme-coupled reaction as previously described (1), in which L-alanine was oxidized to pyruvate and ammonia in the presence of NAD+ and L-alanine dehydrogenase.
Briefly, assay mixture I (1.0 ml; final volume) contained 20 mM L-arginine, 20 mM pyruvate, 0.5 mM PLP, and 70 mM Tris/HCl (pH 9.0), unless otherwise noted. Assay mixture I was preincubated for 10 min at 37°C prior to the addition of 10 µg of recombinant AruH, by which the reaction was started. A 4-min period of incubation at 37°C consumed <10% of the substrates. The reaction was stopped by addition of 50 µl anhydrous hydrazine (Sigma), which trapped the remaining substrate pyruvate (also the reaction product 2-ketoarginine) as the hydrazones. The protein precipitates were removed by centrifugation after assay mixture I was boiled for 10 min. Blanks did not contain L-arginine, pyruvate, or recombinant AruH. Assay I was linear with incubation of the assay mixture for up to 5 min and the enzyme concentration up to 20 µg/ml. For the second step, assay mixture II (2.1 ml) contained 1 ml hydrazine/Tris buffer (hydrazine at 1.0 M, Tris base at 40 mM, EDTA at 1.4 mM, adjusted to pH 9.0 with HCl), 1.2 mM NAD+, and supernatant from reaction I (0.1 to 0.8 ml containing 10 to 100 µM L-alanine). Assay reaction II was started by the addition of 2 U of L-alanine dehydrogenase (Sigma), and the increase in absorbance at 339 nm was monitored at 25°C until no significant increase could be detected. The molar extinction coefficient (6,300 M1 cm1) of NADH was used for the calculation. One unit of enzyme activity was defined as the amount of enzyme that yielded 1 µmol of L-alanine per min under the standard assay conditions described above. Assay II with L-alanine dehydrogenase is specific for L-alanine determination and linear over a range of 5 to 300 µM L-alanine (16). The protein concentration was determined by the method of Bradford (2) with bovine serum albumin as the standard.
Kinetic studies. Kinetic assays were performed by the two-step method as described above, with various concentrations of L-arginine (the amino donor, 2.0 to 10.0 mM) and pyruvate (the amino acceptor, 0.3 to 2.0 mM). Using the kinetics module of SigmaPlot (SigmaPlot 2004 for Windows Version 9.01; SPSS Science), apparent kinetic parameters were determined by fitting data to the equations for sequential and ping-pong steady-state mechanisms, respectively.
Substrate specificity. Substrate specificity was investigated by the assay method described above but by replacing 20 mM L-arginine with various L-amino acids as the amino donors or replacing 20 mM pyruvate with 20 mM 2-ketoglutarate as the amino acceptor. When 2-ketoglutarate was used as the amino acceptor in the reaction, synthesis of L-glutamate was measured by monitoring the formation of NADH from NAD+ in a coupled reaction with L-glutamate dehydrogenase (1). Anhydrous hydrazine (Sigma) was used to trap the remaining substrate 2-ketoglutarate, similar to that used for the arginine:pyruvate transaminase assay.
pH and temperature studies. For pH studies, 70 mM potassium phosphate (pH 6.0 to 8.0), Tris/HCl (pH 7.4 to 9.5), and borate/NaOH (9.0 to 10.0) buffers were used in the assay. Similarly, the temperature dependence of AruH activity was evaluated by incubating assay mixture I for 4 min at 25 to 50°C.
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FIG. 1. Purification of recombinant AruH. Proteins were separated on a 10% SDS-polyacrylamide gel. Lane M, protein markers with sizes shown on the right; lane 1, cell extract before purification; lane 2, the AruH fraction from the affinity column; lane 3, the AruH fraction from the anion-exchange column.
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The purified AruH proteins had a distinct yellow color, suggesting the presence of a bound chromophore. As demonstrated below, AruH possessed a PLP-dependent transamination activity. UV-visible light spectroscopic analysis of AruH revealed an absorption peak centered at 425 nm (data not shown), consistent with the presence of PLP.
Assay of a PLP-dependent arginine:pyruvate transaminase activity of AruH. As described in the accompanying paper (17), several lines of genetic and biochemical evidence led us to propose that AruH possesses arginine:pyruvate transaminase activity. In this reaction, L-arginine and pyruvate served as the amino donor and acceptor, respectively, to make 2-ketoarginine and L-alanine. The amount of L-alanine thus synthesized was measured by the generation of NADH in a coupled reaction by a NAD-dependent L-alanine dehydrogenase as described in Materials and Methods. With this assay, it was found that only negligible L-alanine production could be detected in the absence of PLP, indicating that AruH is a PLP-dependent enzyme.
HPLC and MS analyses were employed to demonstrate the generation of 2-ketoarginine and L-alanine in the proposed reaction by AruH. Two transamination reaction mixtures were prepared, one with active AruH and another with heat-inactivated AruH as a negative control. As shown in Fig. 2, the presence of 2-ketoarginine in the reaction mixture was tentatively identified by HPLC; a peak with the same retention time (5.9 min) as the 2-ketoarginine standard appeared only in the reaction mixture containing active AruH and not in the negative control. However, the presence of L-alanine was difficult to demonstrate by HPLC because of its relatively low molar extinction coefficient (79 versus 1,350 M1 cm1 L-arginine) at 205 nm and the closeness of its retention time (3.36 min) to that of L-arginine (3.42 min) under this elution condition.
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FIG. 2. HPLC analysis of AruH reaction products. Chromatograms of the components of the reaction mixture with either heat-inactivated AruH (dashed line) or active AruH (solid line) were recorded at 205 nm as described in Materials and Methods. Signal peaks were individually identified by comparison to the retention times of authentic reference compounds. In this system, the retention times of L-arginine (L-arg), pyruvate (Pyr), 2-ketoarginine (2-KA), L-alanine, and PLP were 3.42, 4.2, 5.9, 3.36, and 10.8 min, respectively.
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FIG. 3. ESI-MS analysis of the AruH reaction products using L-arginine as the substrate. Panels A and B represent analyses of reaction mixtures with heat-inactivated and active AruH, respectively. The signals with m/z values of 87.0, 88.1, 172.1, and 173.2 were in accordance with the negative ion of pyruvate (Pyr), L-alanine (L-ala), 2-ketoarginine (2-KA), and L-arginine (L-arg).
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Optimal pH and temperature. As shown in Fig. 4, the optimal pH for AruH enzyme activity was 9.0. Borate/NaOH buffer, in this case, showed a strong inhibitory effect on the transamination activity of AruH. The optimal temperature for AruH enzyme activity was 42°C; the enzyme was prone to sharp thermal inactivation above this temperature (data not shown).
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FIG. 4. Effect of pH on AruH activity. The arginine:pyruvate transaminase activities of AruH at pHs 6.0 to 10.0 and 37°C were determined as described in Materials and Methods. The reaction mixture contained 20 mM L-arginine and pyruvate in the following buffers at 70 mM: potassium phosphate at pH 6.0 to 8.0 (filled circles), Tris-HCl at pH 7.5 to 9.5 (open circles), and borate/NaOH at pH 9.0 to 10.0 (filled triangles). For comparison, the specific activity of AruH at pH 9.0 in Tris-HCl was defined as 100%. All experiments were performed in triplicate, and the averages of specific activities were used for comparison.
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FIG. 5. Lineweaver-Burk plot of AruH activities with L-arginine and pyruvate as substrates. Kinetic studies were performed as described in Materials and Methods. (A) The concentration of L-arginine (L-arg, the amino donor) was varied at the fixed concentrations of pyruvate (Pyr, the amino acceptor) indicated. (B) The concentration of pyruvate was varied at the fixed L-arginine concentrations indicated. All experiments were performed in triplicate, and error bars denote standard deviations.
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1-piperideine-2-carboxylate. As expected, no such signal peak was detected in the negative control sample which contained inactivated AruH (Fig. 6). These results indicated that AruH is a transaminase with broad substrate specificity. |
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TABLE 1. Substrate specificity of AruH
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FIG. 6. ESI-MS analysis of AruH reaction products using L-lysine as the substrate. Panels A and B represent ESI-MS analyses of reaction mixtures with heat-inactivated and active AruH, respectively. The signals with m/z values of 87.0, 88.1, 126.1, and 145.1 were in accordance with the negative ion of pyruvate (Pyr), L-alanine (L-ala), 1-piperideine-2-carboxylate, and L-lysine (L-lys).
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-ketoglutarate could substitute for pyruvate as an alternative amino acceptor in the AruH-catalyzed deamination of L-arginine and L-lysine. However, no synthesis of glutamate could be detected in a coupled reaction with NAD+-dependent glutamate dehydrogenase (data not shown). |
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In the Pseudomonas genome annotation (www.pseudomonas.com), AruH was initially described as an aspartate transaminase (AspTA) because of its significant sequence similarities to other bacterial AspTAs, which belong to subgroup I of the transaminase family (7). The AspTAs in subgroup I may be further subdivided into two subgroups, Ia and Ib, according to their mutual homologies (11). AruH showed significant sequence identities (27 to 39%) and similarities (47 to 57%) to AspTAs of subgroup Ib but not with those of subgroup Ia. For AspTAs, an R-292 residue of subgroup Ia (3) or a K-109 residue of subgroup Ib (10) is highly conserved to interact with the distal carboxyl group of aspartate. None of these two residues is conserved in the corresponding sites of AruH, consistent with our conclusion that AruH is not an aspartate transaminase. Since L-arginine is the best substrate for AruH, one would expect the presence of specific interactions between the guanidino group of L-arginine and the side chains of amino acid residues in the catalytic pocket of this enzyme. Future determination of the molecular structure of AruH is expected to answer these questions about the substrate recognition mechanism. It was noteworthy, however, that those amino acid invariants well conserved in AspTAs of subgroup I (8), including Y70, P138, N194, P195, G197, D222, Y225, K258, R266, G268, and A386 (the residues are numbered according to pig cytosolic AspTA), could still be found in the sequence of AruH. Analogous to the roles played by these residues in the members of transaminase family subgroup I, we propose that K-237 of AruH is the active lysyl residue that binds to the coenzyme PLP, D-204 of AruH may form a hydrogen bond to N(1) of the coenzyme, and R365 of AruH may function in binding the
-carboxyl group of substrates.
The conversion of L-arginine into 2-ketoarginine via transamination has been previously reported in Arthrobacter simplex (14). In contrast to the arginine:2-ketoglutarate transaminase of A. simplex, AruH prefers to use pyruvate as the amino acceptor, not 2-ketoglutarate. Those two enzymes are, however, both PLP dependent and showed an arginine-inducible expression profile. Compared to the enzyme of A. simplex, which could utilize L-arginine (100%) but also L-citrulline (16%) and L-alanine (10%), AruH displayed broader substrate specificity and could utilize L-lysine (51%), L-methionine (44%), L-leucine (24%), and L-ornithine (17%) besides L-arginine (100%) as the amino donor. It would be of interest to explore whether AruH plays a role in the utilization of these amino acids and, reciprocally, whether these amino acids exert any effect on the induction of aruH and other genes in the same locus. For instance, production of
1-piperideine-2-carboxylate via transamination between L-lysine and pyruvate, as demonstrated in this report, might provide an alternative pathway for lysine catabolism (12).
This work was supported by National Science Foundation grant 0415608 and by the Molecular Basis of Diseases Program at Georgia State University.
Published ahead of print on 6 April 2007. ![]()
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