School of Dental Sciences, University of Newcastle, Newcastle upon Tyne NE2 4BW, UK
Correspondence
Roy R. B. Russell
r.r.russell{at}ncl.ac.uk
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ABSTRACT |
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INTRODUCTION |
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The extracellular glucosyltransferase (GTF) enzymes that act upon sucrose to produce glucan have a modular structure with distinct catalytic and glucan-binding domains (GBDs) (Colby & Russell, 1997; Monchois et al., 1999
). The C-terminal one-third of GTF has been identified as a GBD and has been shown to be responsible for the ability of GTF to bind dextran, by experiments in which GTF was truncated by protein engineering (Abo et al., 1991
; Ferretti et al., 1987
) and by proteolysis of GTF and capture of dextran-binding fragments (Mooser & Wong, 1988
). The GBD consists of a number of closely related amino acid repeat units that were first demonstrated in GTF-I from a strain originally identified as Streptococcus sobrinus, later reclassified as Streptococcus downei (Ferretti et al., 1987
; Whiley et al., 1988
). GTF-I contains six A repeats of 33 amino acids and two B repeats each of 48 amino acids. A repeats have since been identified in all known streptococcal GTF and in the related dextransucrases of Leuconostoc mesenteroides (Monchois et al., 1996
, 1999
). In addition to the A and B repeats, a variety of different repeating units of varying length and composition have been identified by different authors and named C, D and N repeats (Banas et al., 1990
; Gilmore et al., 1990
; Monchois et al., 1999
). The type and number of repeats vary between different enzymes but only the A repeat appears to be universal (Monchois et al., 1999
; Vickerman et al., 1996
). A distinctive feature of all repeats is the regularly spaced aromatic and glycine residues and it has been suggested that all longer repeats are derived from a basic YG repeat unit (Giffard & Jacques, 1994
). The A repeats show similarity to repeats found in binding proteins in other organisms, notably the choline-binding autolysins and surface proteins of Streptococcus pneumoniae, and the toxins A and B of Clostridium difficile, which are also characterized by conserved aromatic amino acids and glycines (Wren, 1991
; Wren et al., 1991
; Yother & Briles, 1992
; Garcia et al., 1998
; Jane
ek et al., 2000
).
In addition to the GTF, oral streptococci possess several glucan-binding proteins (Gbps) of unknown enzymic activity (Banas & Vickerman, 2003; Matsumura et al., 2003
). Three Gbps have been identified in S. mutans: GbpA (Banas et al., 1990
; Russell, 1979a
), GbpB (Smith et al., 1994
) and GbpC (Sato et al., 1997
). GbpA contains five repeats, similar to those of GTF-I, and deletion of the gbpA gene alters sucrose-dependent biofilm formation in vitro and results in increased caries in a rat model (Banas & Gilmore, 1991
; Hazlett et al., 1998
, 1999
). GbpB and GbpC do not have A repeats and the regions of the molecules involved in glucan binding have not been identified. GbpB appears to be identical to a surface antigen induced by stress and has limited homology to a putative peptidoglycan hydrolase (Chia et al., 2001
; Mattos-Graner et al., 2001
). GbpC is a cell-surface-associated protein involved in dextran-induced aggregation and is expressed only under conditions of stress (Sato et al., 1997
).
Recent advances in genomic and bioinformatics technologies and the availability of the S. mutans genome sequence enable a systematic search for novel Gbps using known glucan-binding sequences as probes in silico. Here we describe the discovery and analysis of a novel glucan-binding protein, GbpD.
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METHODS |
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Molecular biology techniques.
Standard DNA manipulations were carried out using protocols described in Sambrook & Russell (2001). Restriction enzymes were obtained from New England Biolabs and used according to the manufacturer's instructions. Large-scale plasmid extractions for DNA sequencing were carried out using the Plasmid Midi-Kit (Qiagen). DNA sequencing was carried out at the Molecular Biology Unit, University of Newcastle, using Thermosequenase and dye terminator chemistry on an ABI377 sequencer (Amersham). DNA sequence was assembled and analysed using OMIGA v2.0 software (Oxford Molecular). PCR reactions were carried out with the high-fidelity, pre-mixed Extensor Long PCR Master Mix (ABgene) without oil overlays, using cycling conditions recommended by the manufacturer, on a GeneAmp9700 thermal cycler (Applied Biosystems). All PCR primers were custom synthesized by Genset. PCR products for cloning were separated by electrophoresis and purified from the agarose gel using the Qiaex II kit (Qiagen). Electrophoresis of proteins and Western blotting were carried out using the standard protocols described in Sambrook & Russell (2001)
.
Identification of the gbpD gene.
All available GTF and dextransucrase sequences and GbpA (corresponding to 57 individual repeats) were searched by the motif-searching programs MEME and MAST (Bailey & Elkan, 1994; Bailey & Gribskov, 1998
, http://meme.sdsc.edu/meme/website/) to identify the consensus A repeat sequence: WYYFDNNGYAVTGLQTINGQHLYFDANGVQVKG. The TBLASTN program (Altschul et al., 1990
) was used to search the S. mutans UA159 genomic sequence data at http://www.genome.ou.edu/smutans.html to identify ORFs containing matches to the consensus A repeat. ORFs were characterized with the aid of BLASTP and the sequence containing gbpD was recovered with the aid of the Virulogenome website (http://www.vge.ac.uk) and analysed with the commercial packages DNAMan and OMIGA, as well as a range of web-based sequence analysis programs.
Cloning, expression and purification of his-tagged GbpD protein.
A recombinant plasmid expressing GbpD, but excluding the signal sequence, was constructed by PCR cloning of the relevant DNA fragment into the vector pQE30 (Qiagen) such that the coding sequence of the GbpD fragment was in-frame with an N-terminal His6 tag. The primers used were as follows: forward primer DS23 (GCGCAGATCTGACGAGACAGTGATAACTG) incorporated a BglII restriction site (underlined) that gives sticky ends compatible with the BamHI site on the vector; the reverse primer DS24 (GCGCAAGCTTTATTACCTTCTTCGCTGACC) incorporated a HindIII restriction site (underlined) compatible with that on the vector. The His6-tagged GbpD was called GbpD2. For expression and purification of GbpD2, an overnight culture of E. coli cells carrying the expression plasmid was diluted 1 : 20 into 1 litre of 2x YT medium (Muller-Hill et al., 1968) containing ampicillin (100 µg ml1) in a 2·5 l baffled flask and shaken at 37 °C for 1 h. The inducer IPTG was added to a final concentration of 0·1 mM and incubation was carried on for a further 6 h. The induced cells were harvested by centrifugation and resuspended in a total of 5 ml 2x binding buffer (40 mM sodium phosphate buffer pH 7·4, 1 M NaCl) containing Complete Protease Inhibitor Cocktail (Roche Diagnostics). After resuspension, 1 ml of 10x BugBuster cell lysis solution (Novagen) with a few crystals of lysozyme and DNase I were added, and the volume increased to 8 ml with sterile distilled water. The suspensions were frozen at 20 °C overnight. Cleared lysates were obtained by centrifugation and then filtration through a 0·2 µm syringe filter. Imidazole was added to give a final concentration of 20 mM and the volume of the lysate was increased to 10 ml. For affinity purification, an AKTA Prime Chromatography instrument (Amersham Pharmacia) with the pre-programmed HisTag purification protocol was used for subsequent purification steps: the lysate was loaded onto a nickel-charged HiTrap chelating column (Amersham Pharmacia) equilibrated with 1x binding buffer +20 mM imidazole (BBI). After washing with 10 column volumes of BBI to remove unbound material, the his-tagged GbpD derivatives were eluted with an imidazole gradient of 20 mM500 mM and collected in 1 ml fractions. Purity of the fractions was monitored by SDS-PAGE.
Construction of an insertion mutant of gbpD.
An internal fragment from the 5' end of the gbpD coding sequence was PCR amplified from S. mutans UA159 chromosomal DNA using primers designed using the genome sequence. The primers DS21 (TCCCCCCGGGTTGGTTTAGTTTCAGTTGCG) and DS22 (TCCCCCCGGGATGGGGTCTTCTCTGCTTCA) incorporated an XmaI site (underlined) at either end and gave a fragment of 400 bp corresponding to amino acids 16145 of the GbpD sequence. This was cloned into the SmaI site of the suicide vector pVA8912 (Malke et al., 1994
; Simpson & Russell, 1998
) using primer-derived XmaI sites to give plasmid pBal1. S. mutans UA159 cells were transformed with pBal1 using the biofilm transformation method of Li et al. (2001)
. Cells with the plasmid integrated into the chromosome were selected on erythromycin. The correct location of the insertion was confirmed using PCR with primers within the insert and flanking regions.
Binding assays.
To measure binding of dextran by GbpD, the microtitre plate assay of Lis et al. (1995) was modified, utilizing the Ni-affinity of the histidine tag to immobilize the protein (Shah & Russell, 2002
). Cleared lysates of induced E. coli cells carrying the overexpression plasmids or vector controls were prepared as described above. Preliminary experiments revealed that >5 µl of cleared lysate was sufficient to saturate the binding capacity of the Ni-NTA-coated wells (data not shown); therefore as a standard, 50 µl of cleared lysate was added to Ni-NTA-coated 96-well HisSorb plates (Qiagen) in PBS containing 0·05 % (v/v) Tween 20 (PBST) to a final volume of 200 µl and incubated overnight at 4 °C. The protein solutions were removed and the wells washed four times for 1 min with PBST. Two hundred microlitres of a 100 µg ml1 solution of biotin-dextran (Fluka) in PBS +0·2 % BSA was added and incubated for 10 min. After washing as before, wells were incubated with 200 µl of a 1 : 20 000 dilution of Extravidinalkaline phosphatase conjugate (Sigma) in PBS +0·2 % BSA for 30 min and washed again. One hundred microlitres of phosphatase substrate solution (1 mg ml1 p-nitrophenyl phosphate Sigma 104 substrate, 28 mM NaHCO3, 22 mM NaCO3, 5 mM MgCl2) was added and colour change monitored by readings at 405 nm in a Titertek Multiskan MCC 340 Plate Reader. For competition studies, competitors were added and the plates incubated at room temperature for 10 min prior to the addition of biotin-dextran.
Binding of His-tagged GbpD by cells was assayed by a whole-cell ELISA as described by Russell & Beighton (1982). Streptococci from overnight cultures were immobilized in microtitre tray and treated successively with pure recombinant GbpD2, mouse antibody to RGS-His (Qiagen) and finally rabbit anti-mouse alkaline phosphatase conjugate assayed by p-nitrophenylphosphate as above.
Hydrophobicity assay.
Hydrophobicity of S. mutans UA159 and the gbpD mutant was determined by the hexadecane partition assay as described by Hogg & Manning (1987).
Electroblotting and detection with biotin-dextran.
Samples were run on SDS-PAGE and electroblotted onto nitrocellulose membranes. The membranes were kept overnight in 20 mM PBS, pH 7·3, containing 3 % (w/v) BSA (initial heat-shock fraction, Sigma) to block non-specific binding, and washed three times for 15 min in PBST. Biotin-dextran (100 µg ml1; Fluka) in PBS +0·2 % BSA were then added. After incubation at room temperature with shaking, the membranes were washed in PBST for 45 min with three buffer changes and then incubated for 1 h at room temperature with a 1 : 20 000 dilution of Extravidinalkaline phosphatase conjugate (Sigma) in PBS +0·2 % BSA. Proteins that bound to dextran were revealed by a 5-bromo-4-chloro-3-indolyl phosphate/nitro blue tetrazolium colour reaction using reagents supplied by Zymed according to the manufacturer's instructions. Conventional Western blotting was performed with rabbit antiserum raised against purified recombinant GbpD2.
Enzyme activity assays.
Activities on carbohydrates were tested on synthetic substrates linked to 4-methylumbelliferone (4MU). Fluorogenic assays were set up in 96-well microtitre plates as follows. Fifty microlitres of a 100 µg ml1 solution of 4MU--D-glucoside or 4mu-
-D-cellobioside (Sigma) were mixed with 130 µl of 50 mM TES (Sigma), pH 7·5, and either purified GbpD2 (5 µg ml1) or cell-free extract from induced E. coli cells carrying the GbpD overexpression plasmid. The plates were incubated at 37 °C for up to 24 h and fluorescence was visualized under UV light. In each case, cell-free extract from E. coli carrying the pQE30 vector was used as a negative control.
Lipase and esterase activities were tested as above but in the presence of 1 mM CaCl2, on 6,8-difluoro-4MU-octanoate and ELF97 esterase substrate (Molecular Probes), respectively. Lipase activity on triglycerides was tested as follows. The triglycerides were stored as 10 % (v/v) emulsions in 10 % (w/v) gum Arabic and used at a final concentration of 0·5 %. Assays were carried out in buffers made with 50 mM MES, pH 6·5, or Tris/HCl pH 7·0 and 7·5, containing 0·2 % Triton X-100. CaCl2 was added at 1 mM where necessary. E. coli LPS (Sigma; 25 µg ml1 final concentration in the reaction), S. mutans LTA (12·5 µg ml1), S. sanguinis LTA (12·5 µg ml1). LTA from S. mutans and S. sanguinis was prepared as described by Sutcliffe & Hogg (1993) and was kindly provided by Dr S. D. Hogg, University of Newcastle. Cleared lysate from induced cultures expressing GbpD2 was added to the substrate and the reactions were incubated at 37 °C for 24 h. Cleared lysate from cells carrying vector pQE30 were used as the negative control. Lipase activity was monitored by measuring the release of free fatty acids (FFAs) using the Novák assay (Novák, 1965
). For spectrophotometer readings, 200 µl samples of the final colour reaction were transferred to wells in a 96-well microtitre plate and readings taken at 500 nm in a Titertek Multiskan MCC340 plate reader.
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RESULTS |
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Sequence analysis of the GbpD peptide
The gbpD ORF encodes a putative protein of 726 amino acids with a potential 36-amino-acid signal sequence at the N-terminus. The mature peptide is predicted to have a molecular mass of 76 kDa. Fig. 1 shows a schematic illustration of the main features of the peptide and alignments of the relevant motifs. There are three A repeats of which the third is the least homologous to the consensus. The region N-terminal to the repeats does not have any homology to other proteins in the public databases. A BLASTP search showed that the C-terminal region has highest homology (
40 % identity over a 350-amino-acid region) to BglB, encoded by an ORF of unknown function in a region of the S. mutans genome that is involved in utilization of
-glucosides (Cote et al., 2000
) and to polyhydroxybutyrate depolymerases (PHBd). There is also homology to a variety of lipases and esterases. This homology is highest around the lipase box and oxyanion hole motifs typical of lipases and esterases (Bell et al., 2002
). In addition, there are a number of characteristic aspartate and histidine residues after the lipase box that are thought to be involved in co-ordinating the calcium ion necessary for lipase activity and may form part of the catalytic triad with the serine of the lipase box (Arpigny & Jaeger, 1999
). Analysis with the Interpro motif-seeking program (Apweiler et al., 2001
) or a recently described structure modelling server (Dogouet et al., 2002
) also showed that the best matches were to esterases and lipases of the
/
hydrolase family of enzymes. Members of this family show a wide range of substrate specificities (Nardini & Dijkstra, 1999
). Alignment of the lipase box and oxyanion hole of GbpD with various sequences showing similarity is shown in Fig. 1
. These findings suggested that GbpD might be involved in the metabolism of
-glucosides, polyhydroxybutyrate (PHB) or have esterase/lipase activity.
Dextran binding by GbpD
S. mutans strain UA159 was used as the parental strain for insertional inactivation of gbpD as described in Methods. The site of insertion means that residual expression of gbpD would yield only a truncated protein of 100 amino acids, lacking the A repeats and downstream sequences. Both strains were grown overnight and the culture medium was concentrated 50-fold by ultrafiltration after removal of cells by centrifugation. SDS-PAGE and electroblotting of concentrated culture supernatant of S. mutans UA159 with biotin-labelled dextran detected GTF, GbpA and a dextran-binding band of approximately 75 kDa, which correlates well with the calculated molecular mass of 76 kDa for the mature GbpD peptide. This 75 kDa band was absent from the gbpD mutant (Fig. 2
). Specific antiserum raised against GbpD2 detected GbpD in Western blots and also reacted with GbpA and GTF (data not shown). These results confirm that GbpD is expressed, exported and binds to dextran. When sucrose was present in the growth medium, GbpD became cell-associated, as observed previously for other Gbps (Douglas & Russell, 1982
).
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GbpD has homology to esterases and lipases and possesses motifs typical of this family of enzymes. Initial attempts to detect lipase/esterase activity of GbpD carried out using fluorogenic substrates (ELF 97 and 6,8-difluoro-4-methylumbelliferyloctanoate; Molecular Probes) or chromogenic substrates (p-nitrophenylcaproate; Sigma) did not reveal any such activity. The lipase activity of GbpD was also tested by monitoring the release of FFAs from triglyceride emulsions in gum Arabic (Fig. 5). GbpD was able to release FFA from tricaprylin, triolein and to a lesser degree from tricaprin, indicating that GbpD does indeed have a lipase activity. This activity was dependent on the presence of Ca2+ ions. There was no detectable release of FFA in the absence of calcium and activity was abolished by the addition of EDTA.
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Distribution of GbpD
The gbpD gene was first identified in the genome sequence of S. mutans strain UA159. To investigate the distribution of gbpD, PCR reactions using primers DS23 and DS24 (see Methods) were carried out on genomic DNA isolated from a variety of other S. mutans strains. All of 10 strains tested yielded an amplified band corresponding to gbpD of UA159 and expression of GbpD was confirmed by Western blotting with specific antibody. A homologue of the gbpD gene was also found in the partially sequenced S. sobrinus genome (http://www.tigr.org/) but was not found in the partially sequenced genomes of S. gordonii, S. mitis or in any other publicly available complete or partial genome sequences.
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DISCUSSION |
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Clues to a function of GbpD additional to glucan binding came from homology searches with the proposed catalytic domain. The strongest homology was with the BglB protein of S. mutans. BglB is encoded by an ORF in the bgl regulon of S. mutans that is involved in transport and hydrolysis of -glucosides (Cote et al., 2000
). We could not demonstrate any involvement of GbpD in
-glucoside utilization by S. mutans using fluorogenic substrates or
-glucan polymers. It should be noted, however, that an inability to demonstrate a particular enzymic activity with synthetic chromogenic or fluorogenic substrates does not necessarily mean that the activity is not present; for example, streptococcal mannosidases that degrade the Man5 glycan of RNase B failed to degrade 4-methylumbelliferyl- or p-nitrophenol-linked mannoside substrates (Homer et al., 2001
). The function of BglB is not known but it lacks a signal sequence so would be predicted to be in the cytoplasm. It is interesting that S. mutans produces two homologous proteins, one of which is predicted to be extracellular (GbpD) and one that is predicted to be cytoplasmic (BglB) and may have the same substrate specificity.
Since sequence homology with various lipases and esterases was detected, GbpD was subjected to tests for lipase and esterase activities on synthetic fluorogenic and chromogenic substrates. No lipase or esterase activities could be demonstrated using these substrates. However, GbpD was able to release FFAs from triglycerides in the presence of calcium, indicating that GbpD does indeed have a lipase activity. What is the natural substrate for GbpD in its environmental niche? As an extracellular enzyme, GbpD might encounter secreted products of S. mutans itself and the products of other plaque bacteria. Since GbpD is a glucan-binding, lipolytic enzyme, we therefore tested its effect on S. mutans LTA and also LTA of S. sanguinis, which contains diglucosyl-diacylglycerol as the glycolipid substituted with -1,6-linked isomalto-oligosaccharide (Kochanowski et al., 1993
). It has previously been reported that GTF of S. sanguinis interacts with its LTA, presumably through the GBD (Chiu & Baker, 1994
). GbpD2 bound selectively to whole cells of S. sanguinis but not to any other oral streptococci. Furthermore, S. sanguinis LTA was able to compete with biotin-dextran for binding to GbpD and served as a substrate for the lipase activity, with release of FFA. In contrast, S. mutans LTA neither bound nor served as substrate. The specificity of the lipase activity may be due to the fact that GbpD binds to S. sanguinis LTA via the A repeat motif, thereby facilitating access to the ester bond linking the fatty acid moiety. We cannot exclude the possibility that GbpD might attack S. mutans LTA, particularly during growth on sucrose. Under these conditions, GbpD would remain entrapped close to the cell surface within the glucan matrix, which contains both dextran and LTA (Rolla et al., 1980
). If GbpD lipase is active at the cell surface, it might intuitively be expected that reduced lipolysis in the gbpD knockout mutant would result in an increase in hydrophobicity. In fact, the reverse is observed and the mutant is less hydrophobic than the wild-type. It is not yet apparent whether this is due to loss of GbpD protein itself or to a consequential change in the amount or location of other surface components such as lipoproteins. There is close interaction between the various surface macromolecules and alteration in one can have substantial effects on others, with consequences for overall surface properties (Harrington & Russell, 1993
).
Enzymes that can modify or degrade surface LTA have important roles in modulating the surface properties of cells. One such enzyme is Pce, the teichoic acid phosphorylcholine esterase of S. pneumoniae and S. oralis, which is able to remove phosphorylcholine from cell wall teichoic and LTAs (De las Rivas et al., 2001; Ronda et al., 1991
; Vollmer & Tomasz, 2001
). S. mutans does not appear to possess a homologue of Pce and there is no sequence homology between the enzymic domains of GbpD and Pce. Although the first 12 amino acids of the A repeat show high homology to repeats found in Pce and other choline binding proteins of S. pneumoniae (Garcia et al., 1998
; Jane
ek et al., 2000
), this sequence similarity is not reflected in binding specificity and choline was unable to compete with biotin-dextran for binding to GbpD (data not shown). The similarity between Pce and GbpD is thus limited to the fact that both consist of a binding domain and a catalytic domain. All experimental evidence available suggests that the A repeats of GbpD confer specificity of binding only to dextran or LTA containing
-1,6-linked isomalto-oligosaccharide units.
The ability of S. mutans GbpD to release FFAs from another plaque species, S. sanguinis, raises the intriguing possibility that it may modulate the surface of at least one organism within its ecosystem with which S. mutans competes for resources. Such inter-bacterial competition was recently shown to occur between S. pneumoniae and Neisseria meningitidis and Haemophilus influenzae, all pathogens of the human respiratory tract. S. pneumoniae produces a neuraminidase that desialylates the LPS of the other two species, thereby altering their surface properties and rendering them more susceptible to host defences (Shakhnovitch et al., 2002). In normal plaque, S. mutans is rare but in plaque associated with dental caries it is the dominant species. In contrast, S. sanguinis is found in high numbers in healthy plaque but is rare in carious plaque (Becker et al., 2002
). Thus there is a reciprocal relationship between these species. The high proportion of S. mutans in caries-associated plaque has been attributed to its competitive advantage over other plaque species during periods when plaque is at a low pH. Although this may well be a major factor, this study suggests that S. mutans may have another weapon that directly affects competitors and gives it advantage. Furthermore, the pH optimum for the GbpD lipase activity suggests that it will be most effective during periods between sugar exposure, when plaque pH is raised by the buffering power of saliva.
The discovery of GbpD adds to the number of proteins containing a GBD. We have previously reported the antigenic cross-reaction between GTF and GbpA (Russell, 1990) and there is reciprocal cross-reaction between GTF, GbpA and GbpD. One consequence is that any caries vaccine based upon one of these proteins, or an isolated GBD, is likely to have multiple effects upon the growth and properties of S. mutans and proteins of other plaque streptococci with proteins containing A repeats. Identification of the various proteins capable of binding glucans will contribute to our understanding of the complex interactions occurring in plaque.
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ACKNOWLEDGEMENTS |
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Received 2 December 2003;
revised 11 February 2004;
accepted 13 February 2004.