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Applied and Environmental Microbiology, January 2007, p. 312-319, Vol. 73, No. 1
0099-2240/07/$08.00+0 doi:10.1128/AEM.02107-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Departamento de Biocatálisis, Instituto de Catálisis, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain,1 Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain,2 Departamento de Microbiología Molecular, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain,3 Departamento de Microbiología de los Alimentos, Instituto de Fermentaciones Industriales, CSIC, C/Juan de la Cierva 3, 28006 Madrid, Spain4
Received 6 September 2006/ Accepted 29 October 2006
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Nevertheless, the main drawback of the ionic immobilization strategy is the desorption of the proteins during operation, promoting biocatalyst inactivation and product contamination (25, 44). The use of ionic polymers coating the surface of solid supports (e.g., polyethyleneimine [PEI] or dextran sulfate) not only provides a stronger adsorption but also prevents the alteration of the three-dimensional protein structure since the polymer becomes adapted to the enzyme instead of forcing the protein to become adapted to the support (13, 31). The immobilization of proteins on this polymer-coated support may have some additional advantages, preventing subunit dissociation of multimeric enzymes (2, 14, 31) or generating hydrophilic nanoenvironments that stabilize the proteins against the presence of organic solvents (12). However, in some cases a protein may not be adsorbed strongly enough even on these polymeric ionic beds for a particular application. When improving the properties of the support is no longer possible, to further increase the strength of protein adsorption we propose to remodel the enzyme surface by site-directed mutagenesis in order to improve its complementarity with the ionic exchanger, increasing the number of ionic groups in the enzyme surface capable of interacting with the support (that is, exposed to the medium). Therefore, we propose to carry out genetic modifications of the proteins, not to directly improve the enzyme properties (18, 28, 29, 53) but to produce an enzyme with better characteristics to facilitate its immobilization by a very simple technique as its adsorption on anionic exchangers.
This strategy has been used scarcely, and most trials have been directed to control the enzyme orientation on the support (20, 30, 39). Nevertheless, we have recently described the use of Lys-enriched penicillin G acylase (PGA) to establish an intense multipoint covalent attachment to glyoxyl agarose supports (1). However, this technique has not been proposed to be used to improve protein immobilization on ionic exchangers so far. This approach does not require a knowledge of protein structure as deep as that required to directly improve the stability of soluble enzymes, since in this case we only have to be able to predict the groups that will be exposed to the medium. Moreover, it is assumed that site-directed mutagenesis on these surface groups should not cause dramatic negative changes on the enzyme properties (1).
To demonstrate the feasibility of this strategy, we have chosen as a model enzyme the PGA from Escherichia coli (34, 48), one of the most important industrial enzymes because it is currently used by pharmaceutical companies to produce beta-lactam antibiotics (3, 33, 42). Moreover, PGA can be utilized in many other reactions, like enzymatic synthesis of antibiotics, resolution of racemic mixtures, synthesis of amides, and selective deprotections (16, 22, 38, 43, 47, 49-51). PGA suffers a complex posttranslational processing to become active, since it is synthesized in E. coli as an inactive monomer that is autoprocessed during its secretion to the periplasmic space to form an active alpha-beta heterodimer form (23, 52).
In this work, we have increased the number of carboxylic groups in the PGA surface to improve its adsorption on anionic exchangers, where the native enzyme was not significantly adsorbed (M. Fuentes, P. Batalla, V. Grazú, C. C. Benevides, C. Mateo, T. Montes, J. Hermoso, J. M. Guisán, and R. Fernández-Lafuente, submitted for publication). Taking into account that support adsorption may involve a large percentage of the protein surface and even more in the case of polymeric-coated supports where the enzyme may penetrate into the polymeric bed, we have created eight glutamic residues distributed all around the protein surface, trying to reduce the putative negative effects of these mutations on PGA activity or stability.
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Molecular dynamics on PGA enzyme structure.
Models of the different mutants were built on the basis of the crystal structure of the PGA named "OLE_LINK1" from E. coli ATCC 11105 (19). Amino acid changes were introduced using the O graphic program (21) running on a Silicon Graphics workstation. Side-chain rotamers were chosen from a database of more-common conformers (41). First models were energy minimized using the Powell minimizer algorithm implemented in X-PLOR (9), version 3.851. The Engh and Huber (11) force field was used in all energy minimization and molecular dynamic simulations. Subsequently, a slow-cooling molecular dynamic protocol (9) was carried out over a period of 1.5 ps and applied by using a weak temperature coupling method (4). The target temperature of 2,500 K was decreased by 25 K every 100 steps to reach the final temperature of 300 K. The time step was set to 0.005 fs. Finally, the conformation of the different mutants trapped at 300 K was subjected to 500 additional steps of energy minimization.
Bacterial strains, plasmids, and culture media.
Escherichia coli strains DH5
(laboratory stock) and One Shot Top 10 (Invitrogen, Paisley, United Kingdom) were used for routine cloning procedures. Overproduction of PGA was performed on E. coli strain BL21 Star(DE3) (Invitrogen). The E. coli strains were routinely cultured at 37°C in Luria-Bertani (LB) broth, in either liquid or solid media containing ampicillin (150 µg/ml). For overproduction experiments, cells were cultured at lower temperatures to avoid the formation of inclusion bodies (see below). Plasmid pET101/D-TOPO (Invitrogen, Paisley, United Kingdom) was used for cloning purposes according to the supplier's procedures (Invitrogen, Paisley, United Kingdom). Plasmid pOAF, a pET101/D-TOPO plasmid derivative containing the wild-type pac gene from E. coli ATCC 11105, was previously described (1).
Site-directed mutagenesis of PGA.
DNA manipulations were performed as described by Sambrook and Russell (45). PGA mutants were constructed by a site-directed mutagenesis PCR technique (17) using plasmid pOAF as the template and the mutagenic primers shown in Table 1. The eight amino acid changes (Asn or Gln replaced by Glu) were introduced by three PCR steps. First, nine DNA fragments covering the complete sequence of the pac gene and carrying the proposed nucleotide mutations were independently amplified by PCR: fragment A (pOAF as the template and primers P1 and P2R), fragment B (pOAF as the template and primers P2F and P3R), fragment C (pOAF as the template and primers P3F and P4R), fragment D (pOAF as the template and primers P4F and P5R), fragment E (pOAF as the template and primers P5F and P6R), fragment F (pOAF as the template and primers P6F and P7R), fragment G (pOAF as the template and primers P7F and P8R), fragment H (pOAF as the template and primers P8F and P9R), and fragment I (pOAF as the template and primers P9F and P10). Second, these amplified DNA fragments were purified by gel electrophoresis and connected in pairs or triplets by PCR to create four new fragments: fragment AB (fragments A and B as templates and primers P1 and P3R), fragment CDE (fragments C, D, and E as templates and primers P3F and P6R), fragment FG (fragments F and G as templates and primers P6F and P8R), and fragment HI (fragments H and I as templates and primers P8F and P10). Finally, the four DNA fragments (AB, CDE, FG, and HI) were purified by gel electrophoresis and connected all together in a single PCR to reconstruct the mutated pac gene using these fragments as templates and primers P1 and P10. The resulting DNA fragment (ABCDEFGHI), carrying the complete pac gene containing the eight desired mutations, was purified by gel electrophoresis and cloned into plasmid pET101/D-TOPO according to the suppliers (Invitrogen, Paisley, United Kingdom). The resulting plasmid (named pPGA8glu), expressing the mutated pac gene, was completely sequenced to verify the absence of unwanted mutations.
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TABLE 1. PCR primers used for site-directed mutagenesis of the pac genea
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On the other hand, the mutant PGA was purified by fast-performance liquid chromatography by directly loading the dialyzed extract prepared after DNA precipitation on a Q-Sepharose high-performance column (Pharmacia) and eluting the proteins with a gradient of 0 to 200 mM NaCl in 50 mM Tris-HCl buffer, pH 8.5.
Protein concentration was determined by the method of Bradford (7). The purity of proteins was checked on 12% (wt/vol) sodium dodecyl sulfate-polyacrylamide gels as described by Laemmli (27).
Isoelectric point determination.
Analytical isoelectric focusing was performed with a Pharmacia Phast system in a PhastGel IEF, pH 3 to 9 (0.35 mm thin, 5 by 4 cm size, 5% T and 3% C). Running conditions were 2,000 V, 2.5 mA, and 3.5 W at 15°C until 410 V/h was reached. Sample loading was 1 µl per sample (0.150 mg/ml). The gel was stained with Coomassie dye following the supplier's indications, and the isoelectric points of the purified mutant and the wild type were estimated from the positions relative to those of standard proteins (36).
Determination of PGA activity.
Enzyme activity was determined using an automatic titrator (DL50 Mettler Toledo) to titrate the release of phenylacetic acid produced by the hydrolysis of 10 mM penicillin G in 0.1 M sodium phosphate-0.5 M NaCl at pH 8.0 and 25°C. A 100 mM NaOH solution was used as the titrating reagent. One international unit of PGA activity was defined as the amount of enzyme that hydrolyzes 1 µmol of penicillin G per minute at pH 8 and 25°C. All experiments were performed at least in triplicate, and the results are presented as mean values. Experimental error was never over 5%.
In some cases, PGA activity was followed spectrophotometrically using 6-nitro-3-phenylacetamido benzoic acid.
Immobilization on ionic exchangers.
Immobilization was carried out by adding 1 volume of the corresponding supports to 4 volumes of a solution containing 2.5 IU of native or mutant PGA in 5 mM sodium phosphate at pH 7.0 or pH 5.0 at 25°C (standard ratio was 1 g of wet support to 4 ml of enzyme solution). In some cases, immobilizations were carried out in the presence of different concentrations of NaCl.
During adsorption, samples were withdrawn from the supernatant and the suspension to assay enzyme activity as described above. After immobilization, the derivatives were washed with distilled water and stored at 4°C.
Reference suspensions were prepared with exactly the same enzyme concentration and medium conditions (pH, temperature, and ionic strength) but with addition of the corresponding amount of inert agarose instead of the active support. The PGA activity in the supernatant of this reference suspension was fully preserved in all cases; therefore, the decrease in PGA activity observed in the supernatant of the "immobilization suspension" can be directly correlated to the amount of enzyme adsorbed on the ionic exchangers. Experimental error was never over 7%.
Desorption of the proteins adsorbed on the ionic exchangers.
The different immobilized PGA preparations (10 IU/g of support) were incubated at increasing concentrations of NaCl at 25°C and pH 7.0, and after 30 min (longer incubation times did not reveal any change in the results) the PGA activity of the suspension and supernatant was assayed as described above. Experimental error was never over 9%.
Thermal stability assays.
Enzyme preparations (soluble or immobilized preparations) were incubated in 25 mM sodium phosphate buffer, pH 7.0, at 55°C. Samples of the suspension were withdrawn periodically, and enzyme activity was analyzed as described above. PGA residual activity was expressed as a percentage of initial activity at the given incubation time. Experimental error was never over 5%.
Inactivation in the presence of dioxane.
Enzyme preparations were incubated in different percentages of dioxane (vol/vol) in 25 mM sodium phosphate buffer, pH 6.5, at 4°C. Samples of the suspension were withdrawn periodically, and enzyme activity was analyzed as described above. PGA residual activity was expressed as a percentage of initial activity at the given incubation time. Dioxane was used for its deleterious effect on PGA stability and high hydrophobicity, which permit its partitioning when generating hydrophilic nanoenvironments (12). Experimental error was never over 10%.
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FIG. 1. Space-filled model of the three-dimensional structure of the mutated PGA containing eight new Glu residues. Mutated residues are in green. Lys, Arg, Glu, and Asp residues are in dark blue, light blue, red, and pink, respectively. The -subunit of PGA is shown in yellow.
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FIG. 2. pH activity profiles and thermal inactivation courses of both native and mutant PGA. (A) pH activity profiles of enzymes, determined by using penicillin G as the substrate. Experiments were performed at 25°C. (B) Thermal inactivation courses of enzymes. Inactivation experiments were carried out at 55°C in 25 mM sodium phosphate buffer, pH 7.0. Enzyme activity was determined as described in Materials and Methods. Symbols: , native PGA; , mutant PGA.
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TABLE 2. Analysis of ionizable groups of native and mutant PGA accessible to the medium
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FIG. 3. Isoelectric focusing electrophoresis of PGA. Electrophoresis was performed with a Pharmacia Phast system in a PhastGel IEF, pH 3 to 9. Lane 1, pI calibration kit, pH 3 to 9; lane 2, mutant PGA; lane 3, native PGA. The isoelectric points of the purified mutant and wild-type enzymes were estimated from their positions relative to those of standard proteins. See details in Materials and Methods.
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FIG. 4. Immobilization and desorption of PGA on different anionic exchangers. (A) Immobilization courses of native and mutant PGA on different anionic exchangers. White columns, DEAE; gray columns, PEI (25 kDa); black columns, PEI (600 kDa). (B) Desorption of mutant PGA from different ionic exchangers. Immobilizations were performed in 5 mM sodium phosphate buffer, pH 7.0, at 25°C using 10 IU of enzyme/ml support (see Materials and Methods for details). Symbols: , DEAE; , PEI (25 kDa); , PEI (600 kDa).
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Enzyme stability in the presence of dioxane.
Adsorption of the enzymes on polymeric beds has been reported to stabilize the enzymes against the inactivation caused by organic solvents. Figure 5 shows the stabilities of different immobilized preparations of the enzyme in the presence of dioxane. The mutant PGA adsorbed on DEAE was more stable than the enzyme covalently immobilized on CNBr agarose, but the most stable preparations were those where the enzyme was adsorbed on PEI. No differences between PEI-coated supports could be found.
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FIG. 5. Inactivation courses of immobilized mutant PGA in the presence of dioxane. Experiments were carried out in the presence of 60% (vol/vol) dioxane in 25 mM sodium phosphate, pH 6.5, at 4°C. Symbols: , mutant PGA immobilized onto CNBr-Sepharose; , mutant PGA immobilized onto DEAE-agarose; , mutant PGA immobilized onto PEI (25 kDa)-agarose; , mutant PGA immobilized onto PEI (600 kDa).
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On the other hand, the use of a high ionic strength during adsorption to increase the adsorption strength has been reported previously (40), suggesting that these more restrictive conditions make the multipoint adsorption necessary to fix a protein on an ionic exchanger more difficult (26), allowing a better penetration of the enzyme on the polymeric bed.
Thus, to improve the properties of the immobilized PGA on PEI-coated supports (i.e., adsorption strength and stability against dioxane), the adsorption conditions were changed towards apparently less favorable conditions, taking advantage of the new properties of the engineered PGA and the use of a very strong anionic exchanger like PEI. Therefore, enzyme adsorptions under lower pH and higher ionic strength conditions were studied (Fig. 6). At pH 5.0, adsorption of the mutant enzyme was greatly reduced on DEAE (adsorption accounted for less than 40% of the enzyme) and the use of a higher ionic strength further reduced the percentage of adsorbed enzyme. The adsorption on supports coated with 25-kDa PEI under similar conditions produced similar results, although when this support was used the adsorption was slightly higher. Remarkably, the use of PEI of larger sizes (60 kDa or 600 kDa) progressively increases the percentage of immobilized enzyme; in fact, with the largest polymer more than 60% of the enzyme was adsorbed at pH 5.0 and 150 mM NaCl. Figure 6 shows that the mutant PGA adsorbed under these conditions required much higher concentrations of NaCl to be desorbed from the PEI-coated support than when adsorption was performed under standard conditions. The concentration of NaCl required to release 50% of the enzyme from the support increased from 150 mM to 400 mM NaCl. More interestingly, the enzyme adsorbed under the new conditions became much more stable in the presence of dioxane (Fig. 7A), although the thermal stabilities of both preparations were quite similar (Fig. 7B). Therefore, under these conditions, it seems that PGA is able to penetrate deeper inside the polymeric bed.
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FIG. 6. (A) Immobilization at pH 5.0 of mutant PGA on supports coated with PEI (600 kDa). Experiments were carried out in 25 mM acetate buffer, pH 5.0, at 25°C using 10 IU of enzyme/ml support. White columns, 25 mM NaCl; gray columns, 100 mM NaCl; black columns, 150 mM NaCl. (B) Desorption of mutant PGA immobilized at pH 5 on support coated with PEI (600 kDa). Desorption was performed at pH 7 and 25°C as described in Materials and Methods. Activity released from PEI (600 kDa) is depicted as follows: ![]() ![]()
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FIG. 7. Inactivation courses of immobilized mutant PGA. (A) Inactivation by dioxane. Experiments were carried out in the presence of 75% (vol/vol) dioxane in 25 mM sodium acetate buffer (pH 5.5) at 4°C. Symbols: , mutant and native PGA immobilized onto CNBr-Sepharose; , mutant PGA immobilized onto DEAE at pH 7.0; , mutant PGA immobilized onto PEI (600 kDa) at pH 7.0; , mutant PGA immobilized onto PEI (600 kDa) in the presence of 150 mM NaCl at pH 5.0. (B) Thermal inactivation. Experiments were carried out at 55°C in 25 mM phosphate buffer, pH 5.0. Symbols: , mutant and native PGA immobilized onto CNBr-Sepharose; , mutant PGA immobilized onto DEAE at pH 7.0; , mutant PGA immobilized onto PEI (600 kDa) at pH 7.0; , mutant PGA immobilized onto PEI (600 kDa) in the presence of 150 mM NaCl at pH 5.0.
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An enzyme preparation bearing 10 IU (5 g of biocatalyst in 50 ml of reaction mixture) was used at pH 8 and 25°C in the hydrolysis of 5% of penicillin G for 10 consecutive cycles without detecting any change in the enzyme activity, confirming that there is no enzyme desorption under these conditions.
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However, to take full advantage of the immobilization of proteins via ionic exchange, it has been necessary to use highly improved supports (i.e., supports coated with polymeric cationic beds) and, moreover, to use stringent optimized immobilization conditions. In fact, the best results for enzyme stabilization on dioxane and adsorption strength were achieved if the adsorption was performed under apparently unfavorable conditions, i.e., low pH and high ionic strength. The adsorption of the enzyme under more favorable conditions permits the enzyme immobilization just by interaction with the external groups of the polymeric bed, avoiding the possibility that the enzyme could be fully covered by the polymer (40). This may explain the lack of effect of the size of the polymer coating the support on the enzyme stability and adsorption strength (when the enzyme was adsorbed at pH 7.0 and low ionic strength), conditions under which the mutant enzyme becomes fully and rapidly adsorbed even on DEAE-coated supports. However, the use of more restrictive conditions requires the interaction of the polymer with a larger surface area of the protein and involves a high number of groups of the support. In this way, the enzyme may be more extensively covered by the polymer, increasing the protection against inactivation by dioxane and the adsorption strength. The fact that the eight new Glu residues were distributed homogenously throughout the entire enzyme surface contributed to fully cover PGA with the polymer. Thus, in our best optimal preparation the enzyme activity remains fully unaltered after immobilization, and it may be used at a relatively high ionic strength and under a wide range of pH values and present a significant stabilization against the deleterious action of dioxane. Moreover, in spite of this strong adsorption, PGA can be desorbed when it becomes inactivated during operation by incubating the biocatalyst under different conditions (e.g., 100 mM HCl), allowing the reuse of the support for at least five cycles (results not shown).
Thus, reversible immobilization of PGA on supports coated with polymers may permit increase of the stability of the enzyme in the presence of dioxane. Multipoint covalent attachment on proper supports may permit a higher stabilization rigidification of the enzyme, with higher stabilization in thermal inactivations (1, 15, 32). However, the generation of hydrophilic nanoenvironments by this new strategy yields stabilization factors in the presence of dioxane that are very similar to those obtained by multipoint covalent attachment, permitting full use of the advantages of the reversible immobilization.
We kindly appreciate the help of C. Talavera with the isoelectric focusing technique. The help and suggestions of Ángel Berenguer (MCMA, Universidad de Alicante) are gratefully recognized.
Published ahead of print on 10 November 2006. ![]()
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