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Applied and Environmental Microbiology, March 2006, p. 1777-1783, Vol. 72, No. 3
0099-2240/06/$08.00+0 doi:10.1128/AEM.72.3.1777-1783.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Institute of Molecular Biosciences, Massey University, Private Bag 11222, Palmerston North, New Zealand
Received 3 November 2005/ Accepted 20 December 2005
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The core of the PHA granules is composed of high-molecular-weight PHA, for which more than 150 constituents have been identified. PHA granules are surrounded by a phospholipid membrane with embedded or attached proteins consisting of PHA synthase, intracellular PHA depolymerase, amphiphilic phasin proteins, PHA-specific regulator proteins, and additional proteins with yet-unknown functions (for a review, see references 17 and 19). Among these proteins, only PHA synthase is required for PHA granule formation and only PHA synthase was suggested to be covalently attached to the PHA granule core (5). Phasin proteins have recently been subjected to protein engineering in order to enable purification of proteins fused to these proteins, which hydrophobically attach to the preformed PHA granules (3, 4). A previous study showed that the fusion of green fluorescent protein (GFP) to the N terminus of PHA synthase did not interfere with PHA granule formation (14). In this study, we targeted PHA synthase with respect to immobilization of an enzyme at the PHA granule surface. Only PHA synthase is supposed to mediate covalent attachment to the PHA granule surface and hence would enable the design of a robust particle-based recycling system for biocatalysts (20, 21).
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TABLE 1. Bacterial strains, plasmids, and oligonucleotides used in this study
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Overexpression of phaC1 and lacZ-phaC1.
Cells of E. coli BL21(DE3)/pLysS were transformed with plasmids pET14b-phaC1 and pET14b-lacZphaC1. The transformants were grown at 30°C to an optical density at 600 nm (OD600) of 0.6 and then induced by adding isopropyl-ß-D-thiogalactopyranoside (IPTG) to a final concentration of 0.5 mM. After growth for an additional 5 h, the cells were harvested by centrifugation and stored at 80°C.
Excision of the Gm cassette.
P. aeruginosa
phaC1-Z-C2 contained a Gm cassette inserted into the PHA biosynthesis gene cluster. The Gm cassete was removed to avoid polar effects on other genes involved in PHA granule formation. E. coli S17-1 was used to transfer the Flp recombinase-encoding vector pFLP2 (7) into P. aeruginosa
phaC1-Z-C2 strains, and after 24 h of cultivation on MSM containing 5% (wt/vol) sucrose, gentamicin- and carbenicillin-sensitive cells were analyzed by PCR for loss of the Gm resistance cassette.
Complementation of an isogenic-marker-free P. aeruginosa
phaC1-Z-C2 mutant.
For complementation of the PHA-negative mutant, plasmid pBBR1JO5-lacZphaC1 was transferred into P. aeruginosa
phaC1-Z-C2, and transconjugants were selected on MSM containing 150 µg/ml gentamicin (6). The cells were then grown under PHA-accumulating conditions, and the PHA content was determined by gas chromatography/mass spectrometry (GC/MS) analysis.
Determination of PHA synthase functionality.
The functionality of PHA synthase was investigated by analyzing the PHA contents of the respective bacterial cells. The amount of accumulated PHA corresponds to the functionality of PHA synthase. The PHA contents were qualitatively and quantitatively determined by GC/MS after conversion of the PHA into 3-hydroxymethylester by acid-catalyzed methanolysis.
Isolation of PHA granules.
Cells were harvested by centrifugation for 15 min at 5,000 x g and 4°C. The sediment was washed and suspended in 3 volumes of 50 mM phosphate buffer (pH 7.5). The cells were passed through a French press three times at 8,000 lb/in2, and 0.8 ml of the cell lysate was loaded onto a glycerol gradient (88% and 44% [vol/vol] glycerol in phosphate buffer). After ultracentrifugation for 2 h at 100,000 x g and 4°C, granules could be isolated from a white layer above the 88% glycerol layer. The PHA granules were washed with 10 volumes phosphate buffer (50 mM; pH 7.5) and centrifuged at 100,000 x g for 30 min at 4°C. The sediment containing the PHA granules was suspended in phosphate buffer and stored at 4°C.
ß-Galactosidase activity assays.
ß-Galactosidase enzymatic assays were performed as described elsewhere (12). ß-Galactosidase activity is given in Miller units (MU) (12) by using the OD600 of a PHA granule suspension instead of calculating the cell density. To measure the activity of ß-galactosidase at isolated PHA granules, the PHA granule suspension was diluted to an OD600 between 0.3 and 0.4. The results are given as average values of at least three independent experiments.
Kinetics of ß-galactosidase-PHA synthase fusion protein.
A PHA granule suspension with an overall protein concentration of 3.7 µg/ml was used to analyze the enzyme kinetics of LacZ-PhaC1. One unit of ß-galactosidase activity corresponds to the conversion of 1 µmol orthonitrophenyl-ß-D-galactopyranoside (ONPG) to orthonitrophenol per min at 20°C.
ELISA.
For enzyme-linked immunosorbent assay (ELISA), the wells of microtiter plates were coated with 200 µl of a PHA granule suspension and incubated overnight at 4°C. After being blocked with 3% (wt/vol) bovine serum albumin for 1 h, each well was incubated with polyclonal anti-ß-galactosidase antibody conjugated to horseradish peroxidase (Abcam Inc., MA). After each step, the wells were washed several times with phosphate-buffered saline. As a substrate, 200 µl of an o-phenylenediamine solution (Abbott Diagnostics, IL) was added to each well, and after 30 min, the reaction was stopped by adding 0.5 volume of 3 N H2SO4. The amount of substrate conversion was measured at a wavelength of 405 nm using a microtiter plate reader.
SDS-PAGE.
Protein samples were routinely analyzed by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) as described elsewhere (11). The gels were stained with Coomassie brilliant blue G250. Protein bands of interest were cut off the gel and analyzed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).
MALDI-TOF mass spectrometry.
Mass spectrometric analyses of tryptic peptides were carried out on a MALDI VOYAGER DE-PRO time of flight mass spectrometer from PerSeptive BioSystems (Framingham, MA) utilizing a nitrogen laser emitting at 337 nm and an accelerating voltage of 25 kV. Measurements were performed in the delayed-extraction mode using a low mass gate of 2,000. The mass spectrometer was used in the positive ion detection and linear mode. Samples of the digestion mixture were placed directly on a 100-position sample plate and allowed to air dry after the addition of an equal volume of saturated solution of 3,5-dimethoxy-4-hydroxycinnaminic acid (sinapinic acid) in 50% acetonitrile and 0.3% trifluoroacetic acid.
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FIG. 1. Construction of plasmid pBHR80AlacZ.
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FIG. 2. SDS-PAGE analysis of overproduced PhaC1 and LacZ-PhaC1 in E. coli BL21(DE3). Lane 1, molecular mass standard (New England Biolabs, United Kingdom); lane 2, whole-cell lysate of E. coli BL21(DE3) harboring pET14b-lacZphaC1; lane 3, whole-cell lysate of E. coli BL21(DE3) harboring pET14b-phaC1; lane 4, whole-cell lysate of E. coli XL1-Blue harboring pBHR80ALacZ; lane 5, molecular mass standard (New England Biolabs, United Kingdom). The arrows indicate proteins confirmed by peptide mass fingerprinting using MALDI-TOF MS (Table 3).
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TABLE 2. Identified peptide fragments of proteins analyzed by MALDI-TOF MS
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phaC1-Z-
C2 deletion mutant of P. aeruginosa PAO1.
phaC1-Z-C2. The functionality of the PHA synthase was determined by analyzing the PHA content of dried cells using GC/MS, which indicated a PHA content of 70.5% compared with the wild type. The PHA composition showed an increased molar fraction of 3-hydroxydecanoic acid amounting to an additional 15.5 mol% (data not shown).
Localization and display of LacZ at the PHA granule surface.
Since the current model of PHA granule formation suggests that the PHA synthase stays covalently attached to the emerging polyester granule (6, 17), LacZ is presumably exposed at the surface of the PHA granule. To localize LacZ at the PHA granule surface, PHA granules of P. aeruginosa
phaC1-Z-C2 harboring plasmid pBBR1JO5-lacZphaC1 and PHA granules produced by the wild-type P. aeruginosa PAO1 were isolated and used for ELISA. Specific binding of anti-LacZ antibodies to PHA granules isolated from P. aeruginosa
phaC1-Z-C2 harboring pBBR1JO5-lacZphaC1 was suggested by a twofold increase in absorption at a wavelength of 405 nm compared to the wild-type PHA granules. PHA granules formed via LacZ-PhaC1 and PhaC1 mediated absorbances of 0.21 ± 0.015 and 0.1 ± 0.008, respectively.
ß-Galactosidase activity assays.
The LacZ activity was analyzed in order to determine whether LacZ remains active when fused with its C terminus to the N terminus of the PHA synthase and immobilized at the PHA granule surface. LacZ activity could be detected and showed an average of 68,000 MU.
Determination of kinetic parameters of ß-galactosidase immobilized at the PHA granule surface.
In order to determine enzyme kinetics, the ß-galactosidase activities of isolated PHA granules were monitored for 10 min (data not shown). The ONPG concentrations ranged from 50 µM to 500 µM. The correlation of reaction velocity with the substrate concentration could be fitted to Michaelis-Menten kinetics with the aid of nonlinear regression analysis (Sigma Plot enzyme kinetics; systat software, Inc.). A Km of 630 µM and a Vmax of 17.6 nmol/min could be derived.
Mode of protein-PHA granule interaction.
A typical protein profile of PHA granules isolated from the wild-type P. aeruginosa PAO1 is shown in Fig. 3. In contrast, the protein profile of PHA granules produced by P. aeruginosa
phaC1-Z-C2 harboring pBBR1JO5-lacZphaC1 shows an additional major protein with an apparent molecular mass of 180 kDa. MALDI-TOF MS analysis of derived peptides of this 180-kDa protein enabled the identification of LacZ-PhaC1 (Table 2). Interestingly, an additional protein occurred at 116 kDa, which was identified as LacZ by MALDI-TOF MS analysis (Table 2). The nonfused PhaC1 could be detected as a minor protein, which was confirmed by MALDI-TOF MS analysis (Fig. 3). Consistent with previous studies, the PHA synthase attached to PHA granules from wild-type P. aeruginosa PAO1 is only present at low copy numbers and could not be detected as a distinct protein band in SDS-PAGE analysis (10) (Fig. 3). Thorough washing with phosphate buffer containing 0.1% to 1% SDS (wt/vol) did not alter the amount of LacZ attached to PHA granules (data not shown). Harsh conditions (8 M urea, 10 mM dithiothreitol [DTT]) were applied to remove all noncovalently attached proteins. Figure 4 shows an SDS-PAGE analysis of PHA granules produced by P. aeruginosa
phaC1-Z-C2 harboring pBBR1JO5-lacZphaC1, which were subjected to solubilization using 8 M urea and 10 mM DTT. LacZ, as well as other noncovalently attached proteins, was completely removed from the PHA granules, while about 50% of LacZ-PhaC1 was still attached to the PHA granules.
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FIG. 3. SDS-PAGE analysis of PHA granules. Lane 1, molecular mass standard (New England Biolabs, United Kingdom); lane 2, PHA granules from wild-type P. aeruginosa PAO1; lane 3, PHA granules from P. aeruginosa phaC1-Z-C2(pBBR1JO5-lacZphaC1). The arrows indicate proteins confirmed by peptide mass fingerprinting using MALDI-TOF MS (Table 3).
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FIG. 4. SDS-PAGE analysis of PHA granules before and after treatment with 8 M urea. Lane 1, PHA granules from P. aeruginosa phaC1-Z-C2(pBBR1JO5-lacZphaC1) before treatment with 8 M urea; lane 2, PHA granules (insoluble fraction) after treatment with urea; lane 3, proteins (soluble fraction) released from PHA granules after treatment with 8 M urea; lane 4, molecular mass standard (New England Biolabs, United Kingdom). The arrows indicate proteins confirmed by peptide mass fingerprinting using MALDI-TOF MS (Table 3).
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TABLE 3. Determination of enzyme stability of ß-galactosidase at PHA granule surface
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LacZ was chosen in this study as an example of an enzyme to be immobilized. The LacZ was fused via a linker region to the N terminus of the PHA synthase PhaC1 from P. aeruginosa PAO1, which has been studied in detail (1). Production of the complete fusion protein was confirmed using T7 promoter-based overproduction in E. coli and the proper fusion protein, LacZ-PhaC1, was detected by the apparent molecular mass of 180 kDa and MALDI-TOF MS analysis of the respective tryptic peptides (Fig. 1 and Table 2). The lower expression level of the fusion protein versus PhaC1 could be due to the threefold-larger molecular mass of the fusion protein and/or reduced stability of the fusion protein in the absence of PHA granule formation.
LacZ-PhaC1, produced from plasmid pBBR1JO5-lacZphaC1 under lac promoter control, restored PHA biosynthesis in the PHA-negative P. aeruginosa
phaC1-Z-C2 (15). GC/MS analysis indicated that the PHA content was reduced by only about 30% compared with the wild-type PHA synthase, indicating a PHA synthase function of the fusion protein.
PHA granules, whose formation was mediated by LacZ-PhaC1 in the PHA-negative P. aeruginosa
phaC1-Z-C2, were isolated, and LacZ could be localized at the PHA granule surface by ELISA using anti-LacZ antibodies. These PHA granules showed LacZ activity, suggesting that LacZ had been functionally attached to the PHA granule surface. The enzyme kinetics of immobilized LacZ was analyzed by obtaining the reaction velocities at various substrate (ONPG) concentrations, which indicated a Michaelis-Menten reaction kinetics. The Km of 630 µM suggested a high binding affinity, compared with LacZ covalently attached to gold-coated devices (2).
The protein profile of PHA granules mediated by LacZ-PhaC1 showed, in comparison with wild-type PHA granules, three additional prominent proteins, which could be identified as LacZ-PhaC1, LacZ, and PhaC1. Interestingly, the copy numbers of LacZ-PhaC1 and PhaC1 were unusually high, particularly considering that PhaC1 is not detectable by SDS-PAGE analysis of wild-type PHA granule proteins (Fig. 3). Normi et al. (13) described a slight increase in PHA synthase production after introducing a G4D N-terminal mutation in the Cupriavidus necator PHA synthase, which suggested a role of the N terminus in controlling the copy number of the PHA synthase. This study showed that the N-terminal fusion might have stabilized the protein or that the insertion of the lacZ gene at the 5' end of the phaC1 gene might have caused stabilization of the respective mRNA (25). The additional occurrence of LacZ and PhaC1 at the PHA granule surface suggested that the fusion protein might be susceptible to proteolytic digestion in P. aeruginosa (Fig. 3), while the fusion protein is stable in E. coli (Fig. 2). The large amount of LacZ attached to the PHA granules could be due to a stable formation of a functional LacZ heterotetramer with one subunit contributed by LacZ-PhaC1 and three subunits represented by LacZ. This ratio has been suggested by SDS-PAGE analysis (Fig. 3).
To investigate how LacZ interacts with LacZ-PhaC1 at the PHA granule surface, the PHA granules were subjected to solubilization with 8 M urea in the presence of 10 mM DTT. The resulting solubilized proteins and PHA granules were analyzed by SDS-PAGE (Fig. 4), which indicated an almost complete removal of LacZ, while about 50% of LacZ-PhaC1 remained attached to the PHA granules. Thus, LacZ might interact with LacZ-PhaC1 at the PHA granule surface via protein-protein interaction. These data also suggest that one subunit of LacZ-PhaC1, which presumably forms a homodimer (18, 26), remains covalently attached, whereas the other subunit is not covalently attached and can be removed. PHA granules harboring LacZ-PhaC1 were stored for a few months in the presence of protease inhibitor plus or minus 20% (vol/vol) glycerol to investigate the stability of the immobilized LacZ. LacZ activity only dropped to 87% of the initial activity in the presence of glycerol, which suggested that LacZ immobilized at the PHA granule surface remains stable for at least a few months. The purified native LacZ has been described by various commercial producers as stable at 4°C for up to 6 months (http://www.worthington-biochem.com/BG/default.html; http://www.merckbiosciences.com/docs/PDS/345788-000.pdf).
This study demonstrated that protein engineering of PHA synthase provides a platform technology for efficient covalent enzyme/protein immobilization. PHA synthase contains all the inherent properties required for PHA synthesis, as well as PHA granule formation, and can be produced in a variety of organisms (17). These unique properties and covalent binding to the PHA granule make these enzymes ideal tools for functionalization of PHA granules (20) (Fig. 5).
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FIG. 5. Model of in vivo enzyme immobilization using engineered PHA synthase. CoA, coenzyme A.
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We gratefully acknowledge skillful technical assistance by Jane Brockelbank. Proteomic analysis was performed by Simone Koenig (Integrated Functional Genomics, Interdisciplinary Center for Clinical Research, University of Muenster, Muenster, Germany).
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