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Applied and Environmental Microbiology, August 2004, p. 4642-4647, Vol. 70, No. 8
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.8.4642-4647.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
José L. García, and Pedro García*
Department of Molecular Microbiology, Centro de Investigaciones Biológicas, 28040 Madrid, Spain
Received 26 January 2004/ Accepted 21 April 2004
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On the other hand, the use of functional tags to facilitate the purification and immobilization of proteins has been well documented in the literature (30), but there is little data about the fusion of tags to thermophilic proteins (18-20). Most likely, this lack of data is due either to the fact that thermophilic proteins can be partially purified by thermal treatments or that most of the tags described so far for such purposes are thermolabile. In this work, we have investigated the advantages that a novel tag developed by Sánchez-Puelles et al. (25) in the laboratory of J. L. García and P. García might offer. This tag was originally named C-LytA (25) but will referred to hereafter as choline-binding tag (ChB tag). The ChB tag is a 19-kDa protein which corresponds to the choline-binding domain (ChBD) of the major autolysin of Streptococcus pneumoniae (4). This domain is able to specifically bind to choline or its structural analogues (e.g., diethylaminoethanol or DEAE), allowing its purification by affinity chromatography in a single step using choline- or DEAE-containing supports (25). The ChBD has been studied extensively by biophysical and biochemical techniques (15), and its three-dimensional structure was recently elucidated (3). The ChBD has a novel solenoid fold consisting exclusively of ß hairpins that stack to form a left-handed superhelix, known as a ß spiral staircase.
Taking into account the peculiarities of the ChB tag, we have investigated the properties of a novel chimeric protein constructed by fusing this tag to the Pyr from T. thermophilus. This fusion has revealed novel and interesting biotechnological applications for a thermostable tag.
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(6) was used as the host strain. Plasmid pGEM-T easy vector (Promega) was used to clone PCR-amplified DNA fragments; other plasmids used were pCE17 (26), pCUZ1 (26), and pPCR21PYR (kindly provided by A. Haro). E. coli cells were cultured in Luria-Bertani broth containing ampicillin (100 µg/ml) at 37 or 24°C with aeration.
Molecular cloning and sequencing procedures.
Recombinant DNA techniques were conducted by conventional protocols (24). PCR amplification reactionswere performed with 0.5 U of Taq DNA polymerase (Biotools), 0.25 µM concentration of each synthetic primer, 25 µM concentration of each deoxynucleoside triphosphate, and the buffer recommended by the manufacturer. These amplifications were done in a Perkin-Elmer thermal cycler (GeneAmp PCR system 2400). The pyrophosphatase gene was initially amplified from pPCR21PYR with primers PYR5 (5'-CCATCGATCTAGCCCTTGTAGCGGGCGATGC-3') and PYR3 (5'-AACTGCAGGCGAACCTGAAGAGCCTTCCCGTGG-3') (the PstI restriction site is underlined) and cloned into pGEM-T to give rise to pPYRT1. PCR amplification of the thrombin recognition coding sequence, using pCE17 as the template, was achieved using primers Clytnco (5'-CATGCCATGGTATCAAATGCCTTTATCC-3') (the NcoI restriction site is underlined) and Tromter (5'-CGGGATCCTTATTACTGCAGGGAGCCACGCGGAACCAGTTTTACTGTAATCAAGCCATCTGG-3') (the PstI restriction site is underlined). This fragment was digested with NcoI-PstI and inserted into pCUZ1 previously digested with the same enzymes to generate pAPC60. To construct pAPC62, we digested pPYRT1 with PstI-SphI, and the pyr gene fragment was inserted into pAPC60 that had also been cut with PstI-SphI. DNA sequencing of recombinant clones was performed with the Ready Reaction DyeDeoxy Terminator Cycle sequencing kit (Applied Biosystems) and an automatic sequencer (ABIPRISM model 377; Applied Biosystems), using double-stranded plasmids as templates and specific primers.
Enzymatic assay.
Pyr was assayed by the methods of Lanzetta et al. (13) and Verhoeven et al. (33). The assay mixture contained 20 mM Tris-HCl buffer (pH 8.0), 1 mM PPi, and 3 mM MgCl2. This mixture was heated to 80°C, and the enzyme was added. After 5 min at 80°C, the reaction was stopped by placing the reaction mixture on ice. A 50-µl sample was mixed with 800 µl of a 1:3 mixture of 0.045% malachite green hydrochloride and 4.2% ammonium molybdate in 2 N HCl. After 1 min at room temperature, the reaction was stopped with 150 µl of 34% sodium citrate, and the A660 was measured 5 min later. One unit of activity is defined as the release of 1 µmol of phosphate per min at 80°C. The immobilized enzyme in filters or DEAE-cellulose matrix was assayed in a final volume of 10 ml with agitation.
Enzyme purification.
The ChBD-Pyr fusion protein overproduced in E. coli DH5
(pAPC62) was purified on DEAE-cellulose essentially as previously described (25). Briefly, E. coli cells were grown at 24°C for 20 h, harvested by centrifugation, washed, resuspended in 20 mM Tris-HCl buffer (pH 8.0), and broken in a French pressure cell. The crude extract was clarified by centrifugation. The total soluble protein was loaded onto a DEAE-cellulose column equilibrated with 20 mM Tris-HCl buffer (pH 8.0). The column was extensively washed with 20 mM Tris-HCl buffer (pH 8.0) containing 1.5 M NaCl, until no protein was detected in the eluate by the method of Bradford (1) or by measuring the A280. ChBD-Pyr was eluted with 20 mM Tris-HCl buffer (pH 8.0) containing 1.5 M NaCl and 2% choline or with the same buffer containing 1.5% Triton X-100. It is worth noting that the cultures were grown at 24°C to reduce the formation of inclusion bodies.
Enzyme immobilization.
DEAE-cellulose paper filters, 2.3 cm in diameter (Whatman), inserted into a metallic filter holder (Millipore), were equilibrated with 20 mM Tris-HCl buffer (pH 8.0). The enzyme sample was injected inside the holder, and the filter was extensively washed with 20 mM Tris-HCl buffer (pH 8.0) containing 1.5 M NaCl, until contaminant proteins were eliminated. The entire process was performed at room temperature. Next, the filter was withdrawn from the holder to measure the enzymatic activity bound to it. The pH stability assays were performed with 20 mM Tris-HCl buffer (pH 8.0, 7.5, and 7.0) containing 1.5 M NaCl or 20 mM sodium citrate buffer (pH 6.0 and 5.0) containing 1.5 M NaCl.
Analytical ultracentrifugation.
Sedimentation velocity experiments were performed at 50,000 rpm and 20°C in an XL-A analytical ultracentrifuge (Beckman-Coulter) equipped with UV-visible light absorbance optics using double sector Epon-charcoal centerpieces. Differential sedimentation coefficient distributions, c(s), were calculated by least-squares boundary modeling of sedimentation velocity data using the SEDFIT program (28). From this analysis, the sedimentation coefficients of all the sedimenting species were obtained. The latter were corrected for buffer composition using the SEDNTERP program (14) to obtain the corresponding standard values (water and 20°C).
Miscellaneous methods.
Western blot analysis was performed with a polyclonal antiserum against C-LytA, used at a 1:1,000 dilution, as described previously (25). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) (10% or 12.5% polyacrylamide) was performed as described by Laemmli (11), and protein bands were visualized by staining with Coomassie brilliant blue R250.
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(pAPC62) cells. Crude extracts of these recombinant E. coli cells showed remarkable Pyr activity at 80°C, strongly suggesting that the ChBD-Pyr protein maintained its quaternary active structure.
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FIG. 1. Construction of pAPC62. (A) The chbD gene (white boxes), pyr gene (thick black arrows), thrombin recognition coding sequence (tr) (lightly stippled boxes), primers used for PCR amplification (triangles), promoters ( ), and tandem Plpp-lac promoters (![]() ) are depicted. Abbreviations: MCS, multicloning site; Ap, ampicillin resistance gene. (B) Multicloning site sequence of pAPC60. (C) Partial sequence of the recombinant gene chbD-tr-pyr and the corresponding protein. The enzymatic cleavage site of thrombin is indicated by the small arrow.
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FIG. 2. Western blot analysis of the ChB tag and purification of ChBD-Pyr protein. (A) Western blot developed with anti-C-LytA serum. Lanes: 1, crude extract from E. coli DH5 (pAPC60); 2, crude extract from E. coli DH5 ; M, prestained molecular mass markers. (B) SDS-PAGE analysis (12.5% polyacrylamide). Lanes: 1, soluble extract from E. coli DH5 (pAPC62); 2, ChBD-Pyr from DEAE-cellulose chromatography eluted with 2% choline buffer; M, standard molecular mass markers. The gel was stained with Coomassie blue. The positions of molecular mass markers (in kilodaltons) are indicated on the sides of the gels.
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Since it has been suggested that the high ionic concentration of the elution buffer might favor the formation of Pyr oligomeric complexes (7), we tried unsuccessfully to release the fusion protein by using buffers of lower ionic strength, different pHs, or even 6 M urea. However, more than 60% of the ChBD-Pyr protein was released in the presence of Tris-HCl buffer containing 1.5 M NaCl, 2% choline, and 1.5% Triton X-100 (Table 1). It is worth mentioning that the release was due specifically to the combined action of choline and Triton X-100, as ChBD-Pyr was not eluted when the detergent alone was added to the Tris-HCl buffer containing 1.5 M NaCl. This result suggested that ChBD-Pyr protein was bound mainly by specific interactions of the ChB tag with DEAE, but it is most likely that additional strong interactions were produced by multimerization or aggregation of Pyr moieties, creating a highly stable multipoint binding. Such aggregation could be eliminated or reduced in the presence of detergent.
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TABLE 1. Purification of inorganic pyrophosphatase from T. thermophilus
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FIG. 3. Effect of thrombin on the ChBD-Pyr protein. SDS-PAGE analysis (10% polyacrylamide) of purified ChBD-Pyr protein, heated at 70°C for 5 min, and digested with thrombin. Lanes: 1, sample in the presence of 2% choline buffer; 2, sample in the absence of choline; M, standard molecular mass markers. The gel was stained with Coomassie blue. The positions of molecular mass markers (in kilodaltons) are indicated to the left of the gel.
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When a crude cell extract containing the recombinant ChBD-Pyr fusion was passed through a DEAE-cellulose filter, all the protein was retained in this support. After extensive washing of the column with buffer containing 1.5 M NaCl, the chimeric ChBD-Pyr was the single protein retained in this support, as confirmed by SDS-PAGE analysis. Remarkably, the retained protein was very active and could be easily assayed in its immobilized state. However, the specific activity of the chimeric enzyme retained in the paper filter (22,160 U/mg) was lower than that of the soluble enzyme (89,200 U/mg), as well as that of the immobilized enzyme in the particulate DEAE-cellulose support used for chromatographic purposes (95,900 U/mg). This is because the activity of the filter was determined using a typical batch assay without destroying and dispersing the filter matrix. Obviously, under these conditions, the enzymatic activity was not kinetically favored compared to a soluble enzyme or a perfectly disperse suspension of the enzyme bound to a particulate matrix, such as that used for chromatography. Nevertheless, the activity of the enzyme retained in the filter was still very high, and it can be useful for performing different types of assays.
As in the case of the DEAE-cellulose chromatographic matrix, the chimeric protein retained in the filter could be released by the addition of a buffer containing 2% choline plus 1.5% Triton X-100, suggesting that the ChBD-Pyr was retained in the filter matrix by the same type of interactions. In this sense, the ChBD-Pyr protein was also strongly immobilized in the filter, since it was stable at different pHs (from 5 to 8) and after extensive incubation at 80°C or even at 100°C in 20 mM Tris-HCl at pH 8.0. In all these conditions, we could not detect the release of ChBD-Pyr protein from the filter, either by enzymatic or Western blot analyses, although at 100°C, the enzyme progressively lost its activity. These observations confirmed that the ChB tag bound to the DEAE molecules of the paper filter behaves as a thermostable protein, keeping its functional conformation, as occurred with the soluble protein in the presence of free choline (see above).
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In this study, we have explored and exploited the thermophilic properties of the ChB tag by fusing it to an important thermophilic enzyme, such as the Pyr from T. thermophilus. To do this, the ChB tag was improved by the following changes in two traits with respect to those of the original tag (25). (i) The 3' end of the chbD gene cloned into pAPC60 is not truncated, as was the case for the tag encoded by pCUZ1 (25). This change increases the solubility of the ChB tag protein. (ii) The fusion of the thrombin recognition site to the C terminus of the tag allows the release of the native protein from the ChB tag. These advantages, together with the low cost of the chromatographic supports used to purify and immobilize the fused proteins, the high specificity of the binding process, and the versatility of elution buffers, make the ChB tag an attractive alternative compared to other affinity systems. In several aspects, the utility of the ChB tag is comparable to that of the well-known cellulose-binding domain (31), but the new tag provides additional properties and can be used with inexpensive matrixes other than cellulose.
The experimental results reported here on the purification and immobilization of the ChBD-Pyr fusion protein show the versatility of the ChB tag. Our results have shown that the ChB tag was not released from the DEAE-matrix after a thermal treatment, strongly suggesting that the interaction of the protein with the immobilized ligand mimics the situation observed in solution preserving the protein from a thermal denaturation. It is noteworthy that the protein retains its native conformation, since after the thermal treatment not only can it be released by choline but it can be reloaded onto a new DEAE-matrix after dialysis of the choline (not shown). Most likely the DEAE-matrix provides a three-dimensional interaction, with the ChBD occupying at the same time all their choline binding sites and, therefore, mimicking a high concentration of free choline.
Elucidation of the crystal structure of Pyr from T. thermophilus demonstrated that this protein mainly folds as a hexameric molecule (29). More recently, crystallographic analysis of the ChBD of the major LytA autolysin from S. pneumoniae has revealed that this tag can bind four molecules of choline per monomer (3). Thus, theoretically, the hexameric ChBD-Pyr protein can be adsorbed to the matrix through a three-dimensional multipoint interaction with multiple choline-binding sites.
Analytical ultracentrifugation analysis has demonstrated that the multimeric nature of the purified chimeric protein is maintained in the presence of different concentrations of NaCl or choline. Figure 4 shows the sedimentation coefficient distributions c(s) of the ChBD-Pyr protein equilibrated in either 0.2 M NaCl or 1.5 M NaCl plus 2% choline obtained from sedimentation velocity. In both cases, it is clear that the protein sediments as polydisperse samples with a rather broad distribution of species much larger than that of the monomer (3.7S). It is interesting that whereas the aggregation state of Pyr should favor the stability of the immobilized ChBD-Pyr, in this case this property limits the specific elution of the protein by choline from the DEAE matrix. Nevertheless, we have observed that the addition of a mild detergent in the buffer improves its specific elution by choline. The detergent does not eliminate the specific DEAE-ChBD interaction, because the protein cannot be released only by the detergent, but it might relax the Pyr-Pyr oligomer interactions, decreasing the global binding affinity and allowing free choline to favorably compete with DEAE in the choline-binding site of ChBD. The dual behavior of this tag in the absence (thermally unstable) and presence (thermally stable) of choline is a novel property that might be exploited to activate or deactivate fused enzymes. Moreover, the results of proteolytic experiments performed with thrombin confirmed that the thermal stability of the fused ChB tag strongly depends on the presence of choline. It is not infrequent that the proteolytic site created in a tag to facilitate the further release of the native protein was hidden in the folded conformation of the fusion. Although this was the case for the ChBD-Pyr protein, we were able to overcome this problem, because the ChB tag is easily denatured in the absence of choline, making the thrombin site accessible to the protease.
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FIG. 4. Sedimentation coefficient distribution c(s) of the ChBD-Pyr protein. Samples were equilibrated in 20 mM Tris-HCl buffer (pH 8.0) with either 1.5 M NaCl plus 2% choline (solid line) or 0.2 M NaCl (broken line). The arrow shows the theoretical sedimentation coefficient of a protein monomer (3.7S), assuming a spherical shape.
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This work was supported in part by a grant from Fundación Ramón Areces and by a grant from Contrato-Programa de Grupos Estratégicos (BMC2000-1002) de la Comunidad Autónoma de Madrid. C. Moldes received a fellowship from the Fundación Ramón Areces.
Present address: UMR 163, CEA Cadarache, 13108 St. Paul lez Durance, France. ![]()
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