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Journal of Bacteriology, May 2002, p. 2587-2594, Vol. 184, No. 10
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.10.2587-2594.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Department of Microbiology, Institute of Basic Medical Sciences, University of Tsukuba, 1-1-1 Ten-nohdai, Tsukuba 305-8575,1 Biosignal Research Center, Kobe University, 1-1 Rokkodai Nada, Kobe 657-8501, Japan2
Received 26 November 2001/ Accepted 18 February 2002
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Two-component regulatory systems, consisting of a membrane sensor (histidine kinase) and a cytoplasmic response regulator, enable bacteria to sense and respond to environmental conditions. In response to an appropriate signal, autophosphorylation occurs at a conserved histidine residue in the cytoplasmic domain of the sensor. The phosphate group is then transferred to an aspartate residue on the response regulator, which in turn stimulates or represses target genes at the transcriptional level. The importance of these two-component systems, in control of both metabolism and virulence factor regulation, has been demonstrated in a wide range of bacterial species (8).
Previous works have indicated that one of the two-component systems, VirR/VirS, of C. perfringens globally controls the production of the virulence factors alpha-toxin (phospholipase C), theta-toxin (perfringolysin O), kappa-toxin (collagenase), sialidase, protease, and hemagglutinin (18, 27). Studies on virR mutants have also disclosed that the VirR/VirS system regulates the expression of the genes plc (alpha-toxin gene), pfoA (theta-toxin gene), and colA (kappa-toxin gene) at the transcriptional level (5). Banu et al. (3) identified the other genes that were regulated either positively or negatively by the VirR/VirS system by means of a differential display method using the wild type and the virR mutant of C. perfringens.
Proteome analysis is an excellent tool for analyzing the final products of these regulated genes. The profiles of proteome and transcriptome should be different, based on differences in the posttranscriptional regulation that control the translation rate (12) and half-lives of proteins or mRNAs (33), their intracellular location, and their molecular association with other proteins (32).
In this study, we analyzed the secreted proteins that are regulated with the two-component system VirR/VirS by using two-dimensional gel electrophoresis. By comparing the proteome profile of the C. perfringens wild type with that of the virR mutant, 15 proteins were identified as members of the family of VirR/VirS-dependent proteins. One of the VirR/VirS-dependent proteins which showed proteolytic activity was purified and characterized.
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Preparation of extracellular protein fraction. C. perfringens cells were grown in RPMI 1640 medium with and without protease inhibitors at 37°C under anaerobic conditions and harvested at the late exponential growth phase. The cells were harvested by centrifugation at 10,000 x g for 5 min at 4°C. The extracellular proteins in supernatant were precipitated with 10% (wt/vol) trichloroacetic acid overnight at 4°C and centrifuged at 10,000 x g for 5 min at 4°C. The resulting protein precipitate was washed with cold acetone and air-dried.
Two-dimensional electrophoresis. The proteins were treated with a mixture containing 9 M urea, 4% 3-[(3-cholamidylpropyl)-dimethylammoni]-1-propanesulfonate (CHAPS), 100 mM dithiothreitol, and 0.2% (wt/vol) Bio-Lytes 3/10 (Bio-Rad Laboratories, Hercules, Calif.) to obtain completely denatured and reduced proteins. The protein samples were separated using an immobilized pH gradients Ready Strip system (Bio-Rad Laboratories, Hercules, Calif.) in the pH range of 5 to 8 or 3 to 10. For database construction and the identification of proteins by mass spectrometry (MS), 70 to 80 µg of protein was applied. The proteins were silver stained using a Silver Stain II kit (Wako Pure Chemical Industries, Ltd., Osaka, Japan). After the gels were scanned with an imaging system, analysis of the two-dimensional images was performed with the PDQuest software package (Bio-Rad Laboratories, Hercules, Calif.). More than three separate gels of each condition were analyzed, and only spots displaying the same pattern in all parallels were selected for further characterization.
Peptide mass fingerprinting. Peptide mass fingerprinting was performed by the method of Jensen et al. (14) with slight modification. The protein spots were excised with a scalpel and cut into pieces (1 mm by 1 mm). The gel pieces were placed in a microtube and washed in distilled water for 10 min. The gel pieces were washed twice in 25 mM ammonium bicarbonate-50% acetonitrile for 10 min and then once in acetonitrile for 5 min. A minimum volume of 100 mM ammonium bicarbonate was added to totally immerse the gel pieces, followed by incubation for 5 min. An equal volume of acetonitrile was added, incubated for 15 min, and discarded. The gel pieces were dried in a vacuum centrifuge for 30 min.
For enzyme digestion, 1 µg of lysylendopeptidase (Wako Pure Chemical Industries, Ltd., Osaka, Japan) was dissolved in 100 µl of 100 mM Tris-HCl (pH 9.0) and gradually added to the dried gel pieces, followed by incubation for 45 min on ice. After swelling of the gel pieces, the supernatant was discarded, and a minimum volume of 100 mM Tris-HCl (pH 9.0) was added to immerse the gel pieces. Samples were incubated at 37°C for 20 h. After digestion, 40 to 60 µl of 25 mM ammonium bicarbonate was added and mixed for 15 min. Then an equal volume of acetonitrile was added, followed by mixing for 15 min and recovery of the supernatant. From 40 to 60 µl of 5% trifluoroacetic acid-50% acetonitrile was added, the solution was mixed for 15 min, and the supernatant was recovered twice. The extracts were combined, concentrated to about 20 µl by vacuum centrifugation, and supplemented with 80 µl of 0.1% trifluoroacetic acid. The extracts were then concentrated to about 20 µl by an additional vacuum centrifugation.
Before measuring the mass of the peptide mixture, the peptides were purified using a ZipTip C18 (Millipore, Bedford, Mass.) according to the manufacturer's instructions. Purified peptide solution (0.6 µl) was prepared with equal volumes of saturated
-cyano-4-hydroxycinnamic acid in 50% acetonitrile-0.1% trifluoroacetic acid to create a sample template for matrix-assisted laser desorption ionization-time of flight/mass spectrometry (MALDI-TOF/MS) (Voyager Linear DE and Voyager DE RP; PE Biosystems, Foster City, Calif.). Peptide mass fingerprints were analyzed by using Mascot software (Matrix Science, Ltd., London, United Kingdom).
Northern hybridization. Northern hybridization was performed as described previously (5, 16). Chromosomal DNA from C. perfringens strain 13 was used as a template to amplify each DNA fragment by PCR with each primer set (Table 1), except the CPE0163 and CPE0178 genes, according to the DNA sequence data of the C. perfringens genome sequence (28). Plasmids pTS302 (29) and pKY3135 (20) were used as the templates to amplify each DNA fragment by PCR with a universal primer set in the CPE0163 and CPE0178 genes, respectively. Each DNA fragment was labeled with alkaline phosphatase using an AlkPhos Direct kit (Amersham Pharmacia Biotech United Kingdom, Ltd., Buckinghamshire, England) according to the manufacturer's instructions. The qualitative examination of the Northern hybridization analysis data was validated by scanning the blots with a densitometer and determining the relative amounts of each specific transcript with a Quantity One software package (Bio-Rad Laboratories, Hercules, Calif.).
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TABLE 1. Oligonucleotide primers used for PCRa
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Proteases were distinguished through the use of different protease inhibitors. The samples were placed on ice, supplemented with the inhibitors, and left to react for 45 min before adding the proteolytic substrate azocoll. For determination of the proteolytic activity of purified protein, 0.1 mg of bovine serum albumin was added to the assay mixture. One unit of protease activity was arbitrarily defined as proteolysis that resulted in the release of 0.001 absorbance unit of dye for 2 h. Protease specific activities were expressed as units per milligram of protein. Protein concentrations were determined by the Bradford method (Bio-Rad Laboratories, Hercules, Calif.).
Purification of protease. C. perfringens wild-type strain 13 cells were grown in RPMI 1640 medium under anaerobic conditions and harvested at the late exponential growth phase. The cells were harvested by centrifugation at 10,000 x g for 10 min at 4°C. The supernatant was ultracentrifuged at 100,000 x g for 1 h at 4°C. Proteins in the supernatant were concentrated with an Amicon stirred-cell 8050 system and supplemented with a 1/10 volume of 1 M Tris-HCl (pH 7.5)-1.5 M NaCl. Concentrated supernatant solution was applied to a benzamidine-Sepharose 6B (Amersham Pharmacia Biotech United Kingdom, Ltd., Buckinghamshire, England) affinity column (bed volume, 2 ml) equilibrated with 50 mM Tris-HCl (pH 8.0) containing 0.5 M NaCl. The column was washed with 20 ml of the equilibration buffer and eluted with 0.1 M glycine-HCl (pH 3.0). Fractions of 1 ml were collected in a tube that contained 0.3 ml of 0.1 M Tris-HCl (pH 9.0), and the protease activity was assayed.
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The culture supernatant of the wild-type strain 13 and the virR mutant TS133 were collected at the late exponential growth phase, and the proteins were separated by two-dimensional gel electrophoresis. The virR mutant expressed a pattern different from that of the wild type in the pH 5 to 8 gel, as shown in Fig. 1. The virR mutant showed six intensified and four reduced spots compared with the wild strain. This profile was reproducible. The density of the P2 spot was remarkably enhanced in the wild type but absent in the virR mutant. The P4 spot appeared transparent after silver staining in the wild type but was absent in the virR mutant. In the pH 3 to 10 gel, the virR mutant pattern showed three spots with reduced density and two enhanced spots (Fig. 2).
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FIG. 1. Two-dimensional silver-stained gel of proteins in the culture supernatant of C. perfringens strain 13 (A) and the virR mutant TS133 (B). Proteins were separated in the first dimension by a pH 5 to 8 immobilized pH gradient gel and then in the second dimension by a 10% polyacrylamide gel. Reproducible differences in the density of protein spots were examined by at least three independent experiments. Spots were excised, and the corresponding proteins were identified by MALDI-TOF/MS and database searches. The spots are labeled on the gel according to the numbers presented in Table 2.
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FIG. 2. Two-dimensional silver-stained gel of proteins in the culture supernatant of C. perfringens wild-type strain 13 (A) and the virR mutant TS133 (B). Proteins were separated in the first dimension by pH 3 to 10 immobilized pH gradients gel and then in the second dimension by a 10% polyacrylamide gel. Reproducible differences in the density of protein spots were examined by at least three independent experiments. Spots were excised, and the corresponding proteins were identified by MALDI-TOF/MS and database searches. The spots are labeled on the gel according to the numbers presented in Table 2.
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TABLE 2. Summary of proteome analysis, Northern hybridization analysis, and effect of protease inhibitors on the two-dimensional pattern
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FIG. 3. Northern hybridization using various gene probes. The calculated sizes (in kilobases) of the mRNAs are shown at right. Values represent the ratios of specific mRNA levels to those in the wild type. These values are derived from three independent experiments. Lanes: 1, strain 13/pJIR418; 2, strain TS133/pJIR418; 3, strain TS133/pBT404 (virR+) (27). These results are summarized in Table 2.
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Analysis of VirR/VirS-regulated proteolytic activity of culture supernatant. Proteolytic activity of the culture supernatant of C. perfringens was reported to be positively regulated by the VirR/VirS system (18). In the present study, the proteolytic activity of the culture supernatant of the C. perfringens wild type and the virR mutant were determined at the late exponential growth phase. The activity of the culture supernatant of the wild type (2.8 x 105 U/mg) was much higher than that of the virR mutant (1.2 x 103 U/mg). The proteolytic activity of complemented strain TS133(pBT404) was 2.9 x 105 U/mg. In the former, the activity was inhibited by benzamidine, leupeptin, antipain, and EDTA, but it was not affected by phenylmethylsulfonyl fluoride (PMSF), pepstain, phosphoramidon, E-64, or soybean trypsin inhibitor (Table 3).
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TABLE 3. Effect of inhibitors on proteolytic activitya
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FIG. 4. Portion of the two-dimensional pattern of the culture supernatant proteins of the wild type (A), the wild type with benzamidine (5 mM) (B), the wild type with leupeptin (10 µM) (C), and the wild type with antipain (10 µM) (D). The spots are labeled on the gel according to the numbers presented in Table 2.
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FIG. 5. SDS-PAGE analysis of purified protease. Concentrated culture supernatant was applied to a benzamidine-Sepharose 6B column (2 ml) in 50 mM Tris-HCl (pH 8.0)-0.5 M NaCl. The retained enzyme was eluted by applying 0.1 M glycine-HCl (pH 3.0). Fractions of 1 ml were collected and monitored for enzyme activity. Enzyme activity was determined by using azocoll as a substrate. Fractions showing proteolytic activity were pooled. Protein concentration was determined by the Bradford method, and this fraction was subjected to SDS-PAGE analysis under reducing conditions.
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The activity of the purified protease was diminished during 1 week of storage in phosphate-buffered saline at -20°C. The autodigestive degradation of the peptide during storage was also confirmed by SDS-PAGE.
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Among the spots that were apparently different in two-dimensional gel electrophoresis of the wild type and the mutant, 15 spots were found to be the proteins regulated under the VirR/VirS system, and some spots were identified as fragments of the P2 and P5 proteins when analyzed by peptide mass fingerprinting using MALDI-TOF/MS. These fragments are probably derived from cleavage of P2 and P5 by a VirR/VirS-directed protease. The rest of the spots were not so consistently reproducible and therefore were not included in our analysis.
Among these 15 genes, CPE1951, CPE0163, CPE1529, CPE0846, and CPE0173 were positively regulated by the VirR/VirS system at the transcriptional level. The CPE0163 gene was found to be identical to the pfoA gene, and the CPE0846 gene had a consensus sequence that bound to VirR (6, 28). However, the CPE0173 gene, which was identified as the colA gene, and the CPE1951 and CPE1529 genes (28) did not have the consensus sequences to bind VirR. It is probable that the CPE0173, CPE1951, and CPE1529 genes are regulated by a secondary regulator, as in the case of the hyp7 gene, whose expression has been shown to be regulated by the VirR/VirS system (4).
The CPE1231 gene was independent of the VirR/VirS system. The product of CPE1231 had homology with Aas, a surface protein of Staphylococcus saprophyticus (13). This product may be located on the cell surface of C. perfringens and could be released by the VirR/VirS-dependent protease (a product of CPE0846) into the culture supernatant. This may be supported by the following evidence: the P6 protein spot on the two-dimensional pattern disappeared when the culture supernatant was treated with benzamidine, leupeptin, or antipain (data not shown), and the molecular mass of the P6 protein (97 kDa), as estimated by two-dimensional gel electrophoresis, was smaller than that of the product of CPE1231 (122 kDa) (28).
Lyristis et al. (18) measured the proteolytic activity of the culture supernatants of C. perfringens using azocoll as the substrate and found that the activity was regulated by the VirR/VirS system. Award et al. (2) reported that a collagenase gene-defective mutant had very little azocoll activity compared with the wild type. These results suggested that the proteolytic activity of the culture supernatant of C. perfringens using azocoll as the substrate was mostly derived from the collagenase. However, in this study, leupeptin and antipain, which are cysteine protease inhibitors, inhibited 80% of the proteolytic activity in the culture supernatant and did not inhibit the collagenase activity. In the presence of benzamidine, leupeptin, and antipain, the two-dimensional pattern of the wild-type culture supernatant was similar to that of the virR mutant. These results indicated that the culture supernatant contained a VirR/VirS-regulated protease other than the collagenase. In this study, C. perfringens was grown in RPMI 1640, but the other studies used Gifu anaerobic medium (GAM) broth, so the difference is probably due to the use of different culture media. This inference was supported by the increased cysteine protease activity observed in the RPMI 1640 culture supernatant (data not shown).
We used a benzamidine-Sepharose column to purify this protease. The purified protein was homologous with clostripain of C. histolyticum, which is a cysteine protease. The clostripain is a trypsin-like cysteine protease that was specific for the cleavage of arginyl bonds and susceptible to various trypsin inhibitors (23). The purified protease from C. perfringens was also susceptible to trypsin inhibitors such as benzamidine but not to soybean trypsin inhibitor. The substrate specificity of clostripain was similar to that of trypsin; however, clostripain has been shown to preferentially cleave to the carboxyl-terminal side of arginine residues (21). E-64, which inactivates most cysteine proteases (4), did not affect the clostripain. The protease of C. perfringens was also not affected by E-64.
The seven amino acids (FDACLMG) of the active site of the clostripain of C. histolyticum (11) were identical to those of the protease of C. perfringens. The clostripain of C. histolyticum requires calcium ions to enhance its proteolytic activity (22). Similar to this, the protease activity of C. perfringens was reduced with 10 mM EDTA. The presence of the protease in C. perfringens was predicted by a homology search study on the whole genome sequence of the wild strain, using the VirR binding motif as the target sequence (28). It was confirmed in the present study by purification of the clostripain-like protease in C. perfringens.
This work was supported by a Grant-in-Aid for Encouragement of Young Scientists from the Ministry of Education, Culture, Sports, Science and Technology of Japan.
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