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Journal of Bacteriology, July 2008, p. 4859-4864, Vol. 190, No. 14
0021-9193/08/$08.00+0 doi:10.1128/JB.02022-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, 140 Gortner Laboratory, University of Minnesota, St. Paul, Minnesota 55108
Received 31 December 2007/ Accepted 7 May 2008
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-amino acids or drugs. Another gene encoded a homolog of 2-haloacid dehalogenase (HAD). The encoded protein, denoted L-azetidine-2-carboxylate hydrolase (AC hydrolase), was highly overexpressed by subcloning. The AC hydrolase was shown to catalyze azetidine ring opening with the production of 2-hydroxy-4-aminobutyrate. AC hydrolase was further demonstrated to be a new hydrolytic member of the HAD superfamily by showing loss of activity upon changing aspartate-12, the conserved active site nucleophile in this family, to an alanine residue. The presence of a gene encoding a potential export chaperone protein, CsaA, adjacent to the AC hydrolase gene suggested that AC hydrolase might be found inside the periplasm in the native Pseudomonas strain. Periplasmic and cytoplasmic cell fractions from Pseudomonas sp. strain A2C were prepared. A higher specific activity for AC hydrolysis was found in the periplasmic fraction. Protein mass spectrometry further identified AC hydrolase and known periplasmic marker proteins in the periplasmic fraction. A model was proposed in which AC is hydrolyzed in the periplasm and the product of that reaction is transported into and further metabolized in the cytoplasm. |
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AC is toxic to microorganisms if it is transported into the cell and incorporated into proteins (8). However, Saccharomyces cerevisiae is known to detoxify AC via acetylation of the carboxylic acid group (32). Additionally, bacteria are known that not only tolerate AC but use it as the sole source of nitrogen (5, 35, 36). Bacteria growing on AC are reported to open the azetidine ring and susbsequently capture the nitrogen atom via a transamination reaction. The data are consistent with a mechanism involving an enzyme-catalyzed hydrolytic opening of the azetidine ring. However, until the present study, the gene(s) and enzyme(s) responsible for this activity had not been identified. It has also been unclear how cells that metabolize AC might manage to protect themselves against toxic effects of the compound. The present study has addressed those unresolved issues.
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Bacteria capable of growing on AC were isolated by enrichment culture with an inoculum from soil surrounding roots of Lily of the Valley plants. The minimal medium (30) contained 0.4% (wt/vol) glucose as the sole carbon source and 2.5 mM AC as the sole nitrogen source. Liquid cultures were transferred several times and then plated to obtain isolated colonies.
Chemicals and chemical identification. (S)-(–)-Azetidine-2-carboxylate (99%) was obtained from Toronto Research Chemicals, Inc. (North York, Ontario, Canada). o-Phthalaldehyde and (S)-2-hydroxy-4-aminobutyrate were obtained from Sigma-Aldrich (St. Louis, MO). All other commercial chemicals were the highest grade of purity available. Identification of the chemical product of the AC hydrolase reaction and standard compounds was carried out on a Varian VXR 300 MHz nuclear magnetic resonance (NMR) spectrometer. 1H-NMR spectra were recorded with the compound in D2O containing the chemical shift standard 3-(trimethylsilyl)-propionic acid, d4 sodium salt.
Molecular methods.
The Pseudomonas genomic library was created by partial digestion of DNA with EcoRI and ligation into pUC119 using standard methods (24). E. coli strain DH5
cells were transformed with the ligation mixture. Then, the cells were allowed to recover for 45 min, concentrated by centrifugation, resuspended in minimal medium, and plated onto minimal agar containing AC (27). The few colonies observed were picked, inoculated into liquid culture, and then tested for AC hydrolase activity as described below. The putative clones tested positive, and the DNA sequence of the insert was subsequently determined. Inverse PCR was used to extend the flanking DNA sequence beyond the initial 3.4-kb clone obtained in the initial screen, to 7.0 kb (Fig. 1). DNA encoding the putative AC hydrolase was isolated from Pseudomonas genomic DNA by PCR using PfuUltraHS (Stratagene, La Jolla, CA) via the following primers: 5' AZC PCR, GTGGTGGTTCATATGCAACTGACCGACTTCAAAGCG; 3' AZC PCR, GTTGTTGTTCTCGAGTTAGCCCTTCAGCGCTTGCTT ATG. The PCR product was cloned as an NdeI/XhoI fragment into pET29 (Novagen, Madison, WI) and transformed into E. coli strain BLR(DE3) (Novagen) for overexpression of the AC hydrolase. Plates used for selection of clones expressing the AC hydrolase gene were composed of morpholinepropanesulfonic acid minimal medium (19), 1.5% agar, 0.3 M NaCl, 5 mM AC, 1 mM each thiamine, proline, and arginine, and ampicillin.
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FIG. 1. Map of the 7.0-kb region containing the AC resistance and accessory genes. The gene regions represent the following annotated or determined protein assignments (left to right): a GABA permease (perm), GABA aminotransferase, a CsaA export chaperone, the demonstrated AC hydrolase (this study), DMT permease, GABA transporter, DMT permease, and a TetR transcriptional regulatory protein. The region of the 3.4-kb clone is shown at the bottom. The circles represent predicted transcription termination sites (http://www.softberry.com/berry.phtml?topic=fgenesb&group=help&subgroup=gfindb).
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Sequencing and sequence analysis. The 16S rRNA gene from Pseudomonas sp. strain AC and the cloned gene region were sequenced by the University of Minnesota BioMedical Genomics Center using an Applied Biosystems 3100 Genetic Analyzer. Sequence analysis was performed using the program FGENESB (http://www.softberry.com/berry.phtml?topic=fgenesb&group=help&subgroup =gfindb) and the BLAST algorithm to search against the GenBank database (1). For each translated gene product in the AC hydrolase locus, the BLAST hit with the lowest e-value was selected for comparison as presented in the Results section, below.
Separation of cytoplasmic and periplasmic fractions and identification of proteins. Periplasmic and cytoplasmic preparations were prepared by the procedure of Franklin (9). Proteins in each fraction were analyzed by 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and, subsequently, mass spectrometry (MS). Protein bands were eluted from the gel and trypsin treated, and peptides were analyzed by capillary high-performance liquid chromatography and tandem mass spectrometry (MS/MS) as previously described (20). Tandem mass spectra were acquired using a QSTAR Pulsari Q-TOF MS apparatus (ABI, Foster City, CA). Data were analyzed using Mascot v 2.0 (Matrix Science Ltd., Boston, MA) and ProID 1.1/BioAnalyst 1.1/Analyst QS 1.1 (ABI, Foster City, CA). The sequences were run against the NCBI-RefSeq bacterial database from 20 March 2006 with the addition of the AC sequence obtained in this study. The total number of proteins in the final database consisted of 941,110 sequences.
Enzyme assays. AC hydrolase was assayed using a Molecular Devices Gemini XPS spectrofluorimeter (Sunnyvale, CA) to detect primary amines. The procedures were similar to those described for proline reductase (29) with the following exceptions: AC was used in place of L-proline, the reaction mixture was reduced to 0.25 ml and incubated at 35°C, 25 µl of the reaction mixture was added to 1 ml of the o-phthalaldehyde mixture, and 200 µl of each assay mixture was analyzed for fluorescence emission. A standard curve using authentic 2-hydroxy-4-aminobutyrate was linear from 10 to 1,000 nmol.
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Subsequently, bacteria capable of growth on AC as a sole nitrogen source were obtained by culturing bacteria from soil found beneath a well-established bed of Lily of the Valley plants. Luxuriant growth was observed. One bacterium was observed to grow with AC as the sole source of carbon and nitrogen. It was chosen for further study. Morphology, Gram staining, and 16S rRNA sequencing (accession number EU599183) indicated that the bacterium was a Pseudomonas sp., but it did not match any known species closely enough to be given a species name. Hence, it was denoted as Pseudomonas sp. strain A2C.
Identification and cloning of the AC resistance gene region.
AC was found to be toxic to E. coli DH5
strains, and the toxicity was accentuated by the addition of NaCl to the growth medium, as had been observed previously (10, 24, 31). This served as the basis for the selective screening of an E. coli library prepared from total genomic DNA obtained from Pseudomonas sp. strain A2C. It was reasoned that the AC-metabolizing genes, if expressed in E. coli, would protect the cell against growth inhibition by AC. This strategy proved successful.
Putative clones grown on AC-containing agar plates, and thus resistant to AC, were checked for inserts. Several resistant clones were found to contain an identical 3.4-kb insert. Deletion mutagenesis by restriction with EcoR1 resulted in the loss of AC resistance.
Identification of initial product from AC metabolism. A cell-free enzyme preparation from recombinant E. coli containing the intact 3.4-kb insert clone metabolized AC to a water-soluble metabolite. The metabolite reacted with o-phthalaldehyde to produce a fluorescent product. Secondary amines do not produce this product, indicating that the compound was a primary amine. Wild-type E. coli strains did not transform AC to any detectable product.
A primary amine product of AC would only be generated by the cleavage of one of the two different carbon-nitrogen bonds in the azetidine ring. One ring opening would produce 2-hydroxy-4-aminobutyrate (HAB), and the other would yield 4-hydroxy-2-aminobutyrate (homoserine). In this study, NMR spectroscopy unambiguously identified the first detectable metabolite of AC metabolism as HAB [
1.9-2.16 (m, 2H, 3-H), 3.0-3.2 (m, 2H, 4-H), 4.15 (dd, 1H, 2-H, J = 7.5, 4.2)]. The NMR spectrum of the biological material was identical to that of commercially available (S)-HAB. Different HAB enantiomers would be indistinguishable by conventional NMR spectroscopy. The NMR spectrum of authentic homoserine (23) was very different from that of the biological product obtained here. Moreover, (L)- and (D,L)-homoserine were tested in growth experiments and shown not to serve as a sole nitrogen source for Pseudomonas sp. strain A2C.
DNA sequencing and annotation of the AC resistance gene region. The 3.4-kb inserted DNA was sequenced, and then further sequence was obtained from each end to generate a total sequence of 7,001 bp (accession number 1076384) (Fig. 1). Potential open reading frames were found in the 7-kb fragment using BlastX on the NCBI server and the Softberry program FGENESB. Open reading frames were located and annotated as follows: (i) a 4-aminobutyrate (GABA) permease (bp 1 to 219), (ii) an aminotransferase (bp 454 to 1737), (iii) the export chaperone CsaA (bp 1784 to 2113), (iv) a hydrolase of the HAD superfamily shown here to hydrolyze AC (bp 2182 to 2904), (v) a drug/metabolite transporter (DMT) permease family member (bp 2966 to 3835), (vi) a GABA transporter (bp 4041 to 5450), (vii) another DMT permease family member (bp 5687 to 6643), and (viii) part of a TetR family transcriptional regulator (bp 6640 to 7001).
All of the proteins inferred from the 7.0-kb DNA region showed matches to known proteins with a percent sequence identity above 50%, except for one of the putative DMT permeases (Table 1). The two end genes were fragments, but all other translated proteins matched known proteins over the entire sequence length. The highest identities, for the aminotransferase at 66% and the GABA transporter at 76%, were to proteins from other Pseudomonas strains.
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TABLE 1. Sequence analysis of translated putative gene regions in the 7-kb clonea
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Subsequently, the AC hydrolase DNA coding sequence was cloned behind the T7 promoter in E. coli to yield a strain that, when induced, expressed high levels of a 27,000 molecular weight (MW) protein that was ostensibly absent in the wild-type E. coli or in an uninduced recombinant (Fig. 2). The observed major protein migrated in the gel to a position that is close to the predicted molecular weight for the HAD homolog (MW, 27,111). Moreover, higher expression of the 27,000 MW protein led to a dramatic increase in the measured AC hydrolase activity in cell extracts. Whereas the original clone showed a specific activity of 94 nmol per min per mg, the overexpressing clone gave a specific activity of 2,054 nmol per min per mg. The latter protein extract did not show any detectable 2-haloacid dehalogenase activity with either (R)-(+)- or (S)-(–)-2-chloropropionate as the substrate. Moreover, no activity could be detected with L-proline as the substrate.
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FIG. 2. Proteins produced by E. coli strain BLR(DE3) containing a 3.4-kb insert conferring on the bacterium resistance to AC. Protein expression is under control of the T7 promoter. Lanes: (A) uninduced (no isopropyl-β-D-thiogalactopyranoside [IPTG]) cells grown to an absorbance at 600 nm of 0.6; (B) cells induced with IPTG, added initially at an absorbance of 0.6, for 1 hour and reaching an absorbance at 600 nm of 1.3; (C) cells induced with IPTG for 4 h and reaching an absorbance at 600 nm of 2.4. The protein extracts were obtained by boiling whole-cell pellets in SDS and β-mercaptoethanol. The position of the major recombinant protein is shown by the arrow.
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Identification and localization of AC-metabolizing enzymes. The csaA gene adjacent to the identified AC hydrolase gene (Fig. 1), after translation, showed strongest sequence relatedness (Table 1) to a protein from Thermus thermophilus, for which an X-ray structure has been determined and an export-related chaperone function has been established (14, 33). Other strong sequence matches were also identified as putative export chaperones. A related observation was that another Pseudomonas strain that grew on AC accumulated high levels of HAB in the growth medium that were subsequently taken up and metabolized to support growth as a nitrogen source (21). In tandem, these observations supported the hypothesis that the AC hydrolase was transported into, and active in, the periplasm.
To test this hypothesis, cells of the wild-type Pseudomonas sp. strain A2C were disrupted and fractionated into periplasmic and cytoplasmic protein fractions using published procedures as described in Materials and Methods. The polypeptides in each fraction were then separated by denaturing SDS-PAGE (Fig. 3). The periplasmic fraction (Fig. 3A) showed different bands than the cytosolic fraction (Fig. 3B); the latter showed a larger number of protein bands, as expected. The gel regions containing proteins close in molecular weight to the A2C hydrolase (MW, approximately 21,000 to 35,000) in the periplasm and the predicted HAB aminotransferase protein (MW, approximately 42,000 to 52,000) in the cytoplasm were analyzed by elution of polypeptides, digestion with trypsin, and tandem mass spectrometry.
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FIG. 3. SDS-PAGE and tandem mass spectrometry of selected protein bands. (A) SDS-PAGE of periplasmic protein extract and mass spectrum of the peptide in the region of MW 27,000 in the periplasmic fraction and identified as AC hydrolase. (B) SDS-PAGE and mass spectrum of the peptide in the region of MW 46,000 in the cytoplasmic fraction and identified as a homolog to aminohydroxybutyrate aminotransferase. Observed fragment ions are labeled according to the nomenclature of Biemann (3).
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Initial attempts to determine AC hydrolase activity in the periplasmic fraction using the standard fluorimetric assay were confounded by the presence of EDTA in the periplasmic fraction. Removal of the EDTA by dialysis allowed activity to be measured. There was activity in both fractions; however, the specific activity was 40% higher in the periplasmic protein fraction.
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In light of these findings, a putative role for the other gene products is immediately suggested. The product of A2C hydrolytic ring opening, 2-hydroxy-4-aminobutyrate, is proposed to be transported into the cytoplasm by the GABA transporter. The GABA transporter homolog identified in this study showed 76% sequence identity to a similar protein in P. putida KT2440. Transport of HAB by this transporter would allow cytoplasmic metabolism of this intermediate. The present study showed that the aminotransferase was found in the cytoplasm of Pseudomonas sp. strain A2C. The HAB aminotransferase described here showed 66% amino acid sequence identity with the annotated 4-aminobutryate aminotransferase from Pseudomonas syringae (Table 1). The protein identified here also showed 46% amino acid sequence identity to the E. coli 4-aminobutyrate aminotransferase for which an X-ray structure is known (17).
Taken in total, the data suggest the evolution of a multiply tiered strategy for resistance to, and assimilation of, AC. First, if any AC adventitiously enters the cell, a DMT (13) may transport AC outside the cell (Fig. 4). AC in the periplasm is acted upon by AC hydrolase that has been exported outside the cytoplasmic membrane with the possible assistance of the csaA gene product. AC ring opening requires AC hydrolase, and water as a cosubstrate, to produce 2-hydroxy-4-aminobutyrate as the product. 2-Hydroxy-4-aminobutyrate could be transported into the cytoplasm by the action of a GABA transporter homolog and then undergo transamination in the cytoplasm. This not only detoxifies AC but also provides nitrogen to support growth.
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FIG. 4. Proposed model for AC detoxification and assimilation in Pseudomonas sp. strain A2C. The AB transporter is the 4-aminobutyrate transporter; AC is putatively transported out of the cell by the DMT.
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Periplasmic AC hydrolase, mediating both detoxification and catabolism, is relatively unique. Generally, enzymes that catabolize potential growth substrates are not simultaneously protecting against toxins. The most analogous system that we are aware of is a periplasmic catabolic trehalase; however, that protects cells against alginate secreted by the same cell and it is thought to prevent reentry of toxic alginate (2, 9).
We acknowledge Jack Richman for skillful assistance in chemical analyses and for helpful discussions.
Published ahead of print on 16 May 2008. ![]()
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