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Infection and Immunity, September 2001, p. 5494-5501, Vol. 69, No. 9
0019-9567/01/$04.00+0 DOI: 10.1128/IAI.69.9.5494-5501.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
Novel Extracellular x-Prolyl Dipeptidyl-Peptidase
(DPP) from Streptococcus gordonii FSS2: an Emerging
Subfamily of Viridans Streptococcal x-Prolyl DPPs
J. M.
Goldstein,1
A.
Banbula,2
T.
Kordula,3
J. A.
Mayo,1 and
J.
Travis1,*
Department of Biochemistry and Molecular
Biology, University of Georgia, Athens,
Georgia,1 Department of Microbiology and
Immunology, Jagiellonian University, Cracow,
Poland,2 and Department of
Biological, Geological, and Environmental Sciences, Cleveland State
University, Cleveland, Ohio3
Received 20 April 2001/Returned for modification 28 May
2001/Accepted 15 June 2001
 |
ABSTRACT |
Streptococcus gordonii is generally considered a
benign inhabitant of the oral microflora, and yet it is a primary
etiological agent in the development of subacute bacterial endocarditis
(SBE), an inflammatory state that propagates thrombus formation and
tissue damage on the surface of heart valves. Strain FSS2 produced
several extracellular aminopeptidase and fibrinogen-degrading
activities during growth in culture. In this report we describe the
purification, characterization, and cloning of a serine class
dipeptidyl-aminopeptidase, an x-prolyl dipeptidyl-peptidase
(Sg-xPDPP, for S. gordonii x-prolyl dipeptidyl-peptidase), produced in a pH-controlled
batch culture. Purification of this enzyme by anion exchange, gel
filtration, and hydrophobic interaction chromatography yielded a
protein monomer of approximately 85 kDa, as shown by sodium dodecyl
sulfate-polyacrylamide gel electrophoresis (PAGE) under denaturing
conditions. However, under native conditions, the protein appeared to
be a homodimer on the basis of gel filtration and PAGE. Kinetic studies
indicated that purified enzyme had a unique and stringent x-prolyl
specificity that is comparable to both the dipeptidyl-peptidase IV/CD26
and lactococcal x-prolyl dipeptidyl-peptidase families. Nested PCR cloning from an S. gordonii library enabled the
isolation and sequence analysis of the full-length gene. A
759-amino-acid polypeptide with a theoretical molecular mass of 87,115 Da and a calculated pI of 5.6 was encoded by this open reading frame.
Significant homology was found with the PepX gene family from
Lactobacillus and Lactococcus spp. and
putative x-prolyl dipeptidyl-peptidases from other streptococcal
species. Sg-xPDPP may serve as a critical factor for the
sustained bacterial growth in vivo and furthermore may aid in the
proteolysis of host tissue that is commonly observed during SBE pathology.
 |
INTRODUCTION |
Streptococcus gordonii,
classified in the Streptococcus mitis group of oral
streptococci, is a well-studied member of the viridans family of
streptococci (53). These primary colonizers serve a
necessary role in the establishment of microbial communities that are
characteristic of healthy dental plaque. Although considered benign
inhabitants of the oral microflora, viridans members have been
implicated in the systemic disease infective endocarditis (IE)
(9, 26). The progression of this disease state requires (i) trauma (congenital or disease related) to the endothelial valve
surface such that it is predisposed to colonization, (ii) adhesion of
organisms to the modified valve surface after their entry into the
bloodstream via the oral cavity, and (iii) the propagation of infected
vegetation consisting of a fibrin-platelet meshwork (50).
Despite the uniform susceptibility of these streptococci to
-lactam
antibiotics and their lack of classical streptococcal virulence
factors, they can cause life-threatening disease and/or chronic
inflammation with periods of latency and several defined stages
(10, 14)
The ability of these organisms to colonize biofilm surfaces at two
distinct microenvironments has prompted studies of their dynamic
metabolism and patterns of gene expression. Streptococcus sanguinis, studied as a model for viridans pathogenesis, expresses cell surface adhesins and platelet aggregation-associated proteins that
facilitate both colonization and thrombosis at the infected lesion
(12, 15). In addition, metabolic activities have been shown to dictate the availability of cell surface receptors manifested during the recruitment of planktonic bacteria to plaque or the attachment to a new biofilm surface (4, 12). Upon entry
into the bloodstream, bacteria undergo a shift in pH from mildly acidic plaque (6.0 to 6.5) to the neutral pH (7.3) of the blood
(41). In vivo expression technology was employed on the
S. gordonii rabbit model of IE to detect genes activated in
the new environment, with the alkaline shift in pH correlating with
enhanced bacterial growth, upregulation of the msrA
oxidative stress gene (52), and the induction of genes
encoding carbohydrate metabolism enzymes, protein transporters, and
cell surface proteins (22). The expression and secretion
of glycosidase and peptidase activities, as examined in pH-controlled
batch cultures, was found to be down-regulated by acid growth
conditions and up-regulated by growth in a neutral pH environment
supplemented with serum (13). Chemostat growth also
uncovered a pH-dependent thrombin-like activity, which was considered
more important in the tissue model than on tooth surfaces (32). This could reflect selective pressure for the
organism to adapt novel enzymatic mechanisms for a changing environment.
It is presumed that S. gordonii obtains necessary protein
nutrients from salivary glycoproteins in the oral cavity, while it
utilizes plasma proteins when growing on heart surfaces. This use of
plasma proteins by oral streptococci as carbon and nitrogen sources would ostensibly benefit growth in the vegetation. Certainly, proteolytic and peptide transport systems for viridans members have
been described (1, 7, 17, 18, 25, 45, 54), and it has been
shown that small peptides can be imported into S. sanguinis,
while those exceeding size limitations would require further hydrolysis
by endo- and exopeptidases present on the surface or secreted by these
cells (8). One such activity that facilitates these
metabolic requirements, a dipeptidyl peptidase (DPP) with Gly-Pro-pNa hydrolyzing activity, has been detected in
culture supernatant of S. gordonii (8, 19) yet
has remained undefined. In this report we describe the purification,
characterization, and cloning of a novel extracellular x-prolyl DPP
that derives from S. gordonii FSS2 (Sg-xPDPP), a strain
previously isolated from the bloodstream of a patient with subacute
bacterial endocarditis (SBE).
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MATERIALS AND METHODS |
Materials.
H-Gly-Pro-pNa,
H-Arg-Pro-pNa, H-Ala-Ala-pNa,
N-Suc-Gly-Pro-pNa, L-Pro-pNa,
H-Gly-Arg-pNa, H-Gly-pNa,
Sar-Pro-Arg-pNa, Di-isopropyl fluorophosphate (DFP),
N
-p-tosyl-L-lysine-chloromethyl
ketone (TLCK),
N
-p-tosyl-L-phenylalanine
chloromethyl ketone (TPCK), iodoacetamide,
O-phenanthroline, aprotinin, bestatin, apstatin,
-mercaptoethanol, Gly-Pro-Arg-Pro-amide, sexual agglutination peptide, sleep-inducing peptide, substance P,
des-Arg1 bradykinin, bradykinin, kallidin,
lymphocyte-activating pentapeptide fragment, and fibrin polymerization
inhibitor were obtained from Sigma. Pefabloc SC, phenylmethylsulfonyl
fluoride (PMSF), 3,4-dichloroisocoumarin, and E-64 were from Boehringer
Mannheim. Z-Ala-Pro-pNa, H-Ala-Ala-pNa, H-Ala-Phe-pNa, H-Lys-pNa, H-Arg-pNa,
protein kinase C fragment, Arg-Pro, and fibrin inhibitory peptide
were from Bachem. Protein kinase C peptide was from American Peptide
Company. Human RANTES, MIP-1
, and granulocyte-macrophage
colony-stimulating factor were from PeproTech. H-Glu-(NHO-Bz)
pyrollidide and diprotin A were from Calbiochem.
-1-Proteinase
inhibitor and
-2-macroglobulin were gifts from Athens
Research and Technology (Athens, Ga.).
Bacterial growth.
S. gordonii FSS2 (previously
called S. sanguinis FSS2 [29]) was
stored and maintained (at
80°C) as previously described (32). Frozen cells were inoculated into autoclaved medium
containing 20 g of trypticase peptone (BBL)/liter, 5 g of
yeast extract (Difco)/liter, 2 g of NaCl/liter, 0.1 g of
CaCl2/liter, 4 g of
K2HPO4/liter, and 1 g
of KH2PO4/liter. Glucose
(10 g/liter) and L-arginine (0.5 g/liter) were sterile filtered and subsequently added. A static culture
(200 ml) was grown overnight at 37°C and used to inoculate a 4-liter
starter culture, in turn used to inoculate a 15-liter stirred batch
culture which was grown in an atmosphere of 5%
CO2 and 95% N2 at 37°C
with the pH held constant at 7.5 by addition of 5 M KOH using a pH
controller (Cole Parmer). Cultures were harvested in early stationary
phase at a point when the bacteria had metabolized all available
glucose and the addition of base had ceased.
Enzymatic assay
Amidolytic activities of
crude samples and purified protease were measured using the substrate
H-Gly-Pro-pNa (1 mM final concentration) in assay buffer
A (50 mM Tris, 1 mM CaCl2 [pH 7.8]) at 37°C. Assays were performed in 0.1 ml on 96-well plates using a thermostated microplate reader, and the release of p-nitroaniline was
measured at 405 nm (Spectramax; Molecular Devices). Inhibition assays
involved preincubation of pure enzyme with inhibitor for 10 min at
37°C followed by measurement of residual activity. Additional
pNa substrates were treated identically.
Enzyme purification
Cell-free culture
filtrate (14.5 liters) was obtained after centrifugation (20 min, 4°C
at 6,000 × g) of the batch culture. Proteins in
the filtrate were precipitated over several hours at 4°C with
ammonium sulfate to a final concentration of 80%, and the precipitate
was pelleted by centrifugation at 8,000 × g for 40 min. Protein pellets were obtained upon centrifugation as previously
described. Pellets were resuspended in 200 ml of buffer A and dialyzed
over 2 days (4°C), with changes, against 40 volumes of the same
buffer. All column chromatography steps were performed at 4°C, except
for fast protein liquid chromatography (FPLC) separations that were
done at room temperature. The dialyzed fractions were applied to a DE52
(Whatman) column (2.5 by 30 cm, 150 ml) equilibrated with buffer A. The
column was washed with 3 column volumes of buffer A at 1 ml/min. A
gradient from 0 to 1 M NaCl in buffer A was applied over a total volume
of 700 ml. Peak activity that eluted was pooled and concentrated by
ultrafiltration to 32 ml by using a 10K membrane (Filtron). The
concentrated sample was divided into three equal fractions that were
separately loaded onto a Superdex 75 HR 10/30 (Amersham Pharmacia
Biotech) equilibrated with gel filtration buffer (50 mM Tris, 200 mM
NaCl, 1 mM CaCl2, 0.02% sodium azide [pH 7.8]) at 1 ml/min. Peak activities of all runs were combined and concentrated to
22 ml. Ammonium sulfate was added to the fraction in order to give a
final salt concentration of 1 M. This sample was then applied to a
phenyl-Sepharose HP column (1.5 by 9 cm, 15 ml) equilibrated with 200 mM potassium phosphate-1 M ammonium sulfate (pH 7.5) at 0.5 ml/min.
The column was washed with high-salt buffer (120 ml) until an
A280 baseline was reached and then was
subjected to a 250-ml gradient of 1.0 to 0.0 M ammonium sulfate
utilizing 50 mM potassium phosphate (pH 7.5). Active fractions were
pooled and dialyzed against 20 volumes of buffer A over a 24-h period.
The dialyzed sample was concentrated to 37 ml and then applied to a
Mono Q HR 10/10 fast protein liquid chromatography column (Amersham
Pharmacia Biotech) that was equilibrated with buffer A. The column was
washed with equilibration buffer until the baseline stabilized. A
linear gradient (0 to 500 mM NaCl in buffer A) over 100 ml was applied,
and peak enzyme activity was eluted between 200 and 250 mM NaCl. This
activity was pooled, dialyzed against 10 volumes of buffer B (25 mM
Tris, 5 mM CaCl2 [pH 7.4]), and applied to a Cibacron
blue Sepharose CL-6B column (1 ml) equilibrated with buffer B. Activity
flowed through the matrix and was collected while bound, and
nonspecific protein was eluted in high-salt buffer B. Final
purification to remove additional contaminants involved the use of a
Gly-Pro Sepharose affinity column (1 ml). Enzyme obtained from the
previous step was loaded onto the column that was previously
equilibrated with buffer B. It was then washed with 10 column volumes
of this buffer, and a linear gradient (0 to 1 M NaCl in buffer B) over
30 ml was applied. Peak activity was eluted between 150 to 200 mM NaCl
and was concentrated to 2.5 ml using a 10K Microsep.
Protein determination
Protein concentration
was determined using a bicinchoninic acid reagent kit (Sigma) according
to the manufacturer's protocol.
Electrophoresis and autoradiography
Enzyme
purity was determined by sodium dodecyl sulfate-polyacrylamide gel
electrophoresis (SDS-PAGE) using a 10% acrylamide gel and the
Tris-HCl/Tricine buffer system, according to the method of
Schägger and von Jagow (49). Nondenaturing gel
electrophoresis (48) in a 4 to 20% gradient gel and gel
filtration were used to obtain the molecular weight of the native
protein. To confirm the identity of Sg-xPDPP as a serine protease, 5 µg of pure enzyme was incubated with 500 nCi of
[1,3-3H]DFP for 30 min at 25°C in 20 mM HEPES, pH 7.5. Cold DFP (10 mM final concentration) was used to quench the reaction
and labeled protein was run on SDS-PAGE, followed by fixing in
2,5-diphenyloxazole, drying of the gel, and exposure to X-ray film
(XAR; Eastman Kodak) over a 96-h period. For amino-terminal sequence
analysis, Sg-xPDPP was resolved by SDS-PAGE, followed by
electroblotting to a polyvinylidene difluoride membrane using 10 mM
3-(cyclohexylamino) propanesulfonic acid-10% methanol, pH 11 (30). The blot was air dried and the band was submitted
for sequencing.
Enzyme kinetics and specificity.
Kinetic values were
measured using H-Gly-Pro-pNa at various concentrations
ranging from 20 µM to 10 mM, with a fixed enzyme concentration at 2 nM, in 100 mM Tris (pH 7.8) at 37°C.
Vmax and Km values were obtained through hyperbolic
regression analysis (shareware from J. S. Easterby, University of
Liverpool, Liverpool, United Kingdom). Specificity studies utilized
Sg-xPDPP incubated with 5 µg of peptide in a 1:1,000 molar ratio.
Reactions occurred in 100-µl volumes with 100 mM Tris (pH 7.8) at
37°C for 2 h. Digestions were terminated by acidification with
10 µl of 10 M HCl followed by centrifugation (10,000 × g, 5 min). The entire supernatant was applied to
reverse-phase high-pressure liquid chromatography (HPLC) using an LC-18
column (25 by 4.6 mm, 5 µm) (Supelco) equilibrated with 0.1%
trifluoracetic acid in HPLC-grade water and developed with an
acetonitrile gradient (0 to 80% in 0.08% trifluoracetic acid over 50 min). Peaks were manually collected and analyzed by mass spectrometry.
Mass spectrometry
Peptides and native
Sg-xPDPP were analyzed by matrix-assisted laser desorption ionization
(MALDI)-time of flight on a Hewlett-Packard G2030A mass spectrometer.
The instrument was operated at an accelerating voltage of 28 kV, an
extractor voltage of 7 kV, and a pressure of 9.33 × 10
5
Pa. Samples were dissolved in sinapic acid and ionized from the probe tip using a nitrogen laser source. Calibration was performed using mixtures of peptides and proteins of known molecular masses.
N-terminal and internal sequencing
Proteins
and peptides were sequenced by Edman degradation in a model Procise-cLC
sequencer (PE Biosystems, Foster City, Calif.) operated using the
manufacturer's protocol. For internal sequencing, proteins were in-gel
digested with trypsin (sequence grade; Promega) and the peptides were
extracted (46), with their masses being determined by
reflectron MALDI-time of flight mass spectrometry using a Bruker
Daltonics ProFlex instrument (42). Selected peptides were
sequenced by Edman degradation.
Cloning of Sg-xPDPP gene.
DNA from S. gordonii was purified using the Purgene DNA isolation kit (Gentra,
Minneapolis, Minn.) according to the manufacturer's instructions. The
N-terminal fragment of the xPDPP gene was obtained using a PCR
approach, and degenerate primers were designed for the N-terminal
(MRYNQY) and internal (NVIDWL) peptides. Two putative N-terminal
primers and one internal primer (all containing BamHI sites
[underlined]) were synthesized (nt-1-dpp,
5'-CGCGGATCCATGCGNTAYAAYCARTA-3'; nt-2-dpp,
5'-CGCGGATCCATGAGRTAYAAYCARTA-3'; and int-1-dpp,
5'-CGCGGATTCARCCARTCDATNACRTT-3', respectively). PCR was performed using Pwo DNA
polymerase (Roche Molecular Biochemicals, Indianapolis, Ind.), 1 µg of S. gordonii DNA, and 500 ng of the primers (94°C
for 1 min, 65°C for 1 min, 72°C for 1 min, 32 cycles). A single
965-bp-long PCR product was obtained, gel purified, digested with
BamHI, subcloned into the BamHI site of
pUC19, and sequenced. The obtained sequence was used to search
the unfinished S. gordonii database, available at The
Institute of Genomic Research (TIGR) website
(ftp://ftp.tigr.org/pub/data/s_gordonii/). Several overlapping
contigs were found, and this approach resulted in the identification of
a 2,280-bp-long open reading frame (ORF) carrying the Sg-xPDPP gene.
Subsequently, two PCR primers encoding the N and C termini of DPPIV
were synthesized (5'-AGTGGATCCATGCGTTACAACCAGTATAG-3' and
5'-TTTGGATCCTCAAGATTTCTTGTGAGGC-3') and
used in the PCR to obtain the full-length DNA fragment encoding DPPIV.
The 2,298-bp-long PCR product was gel purified, digested with
BamHI, subcloned into the BamHI site of pUC19,
and sequenced on both strands.
Nucleotide sequence accession number.
The sequence obtained
for the Sg-xPDPP gene was deposited in GenBank under
accession number AY032733.
 |
RESULTS |
Enzyme purification.
Earlier growth experiments indicated the
presence of an extracellular Gly-Pro-pNa activity in culture
media. Detection of this amidolytic activity in cell-free filtrate was
dependent upon growth maintained in a pH range of 6 to 7.5 (unpublished
results). In this report, maximum activity was achieved using a
14.5-liter batch culture held at pH 7.5 by addition of base and
harvested during early stationary growth. An 80% ammonium sulfate
precipitation concentrated extracellular proteins to a workable volume
despite the large decrease in enzymatic yield. The subsequent
chromatographic steps (DE52 anion-exchange, Superdex 75 gel filtration,
and phenyl-Sepharose hydrophobic chromatography) successfully removed
high- and low-molecular-weight contaminants, medium pigments, and
peptides and amino acids away from the Gly-Pro-pNa activity
with a minimal drop in yield. The Mono Q step increased specific
activity by 16-fold, although the yield was reduced 50%. CB Sepharose
chromatography served as a negative step, enabling activity to flow
through the matrix while higher-affinity proteins and
glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (40)
remained bound. The final step, utilizing Gly-Pro Sepharose, resulted
in a single, sharp peak of purified protein. Concentrated fractions
corresponded to high specific activity, a greater than 6,000-fold
purification, and 1% yield from the starting batch culture (Table
1).
Physical properties.
SDS-PAGE analysis of the purified enzyme
(Fig. 1) showed a single protein band, as
judged by both Coomassie and silver staining (the latter is not shown),
with an approximate mass of 85 kDa. Analysis of the protein by MALDI
revealed a laser intensity peak that corresponded to a mass of 86,977.6 Da. Protein analyzed on a 4 to 20% native gradient gel and Superdex
200 gel filtration indicated a molecular mass between 150 and 200 kDa,
providing evidence for homodimer formation in the native state. This
was ablated by heat treatment, SDS denaturation, and MALDI analysis. This suggested that the dimer was stabilized by weak
ionic-electrostatic conditions. Isoelectric focusing (data not shown)
produced a pI of 4.9 for the native protein. The Gly-Pro-pNa
activity was optimum at pH 8.0, with activity detected over a broad
phosphate buffer range of 5.0 to 10.0. The optimum temperature for
Gly-Pro-pNa hydrolysis was determined to be between 45 and
50°C. The enzyme in its pure form was unstable over a 15-h period at
37 and 25°C (complete loss of activity) and at 4°C (75% loss of
activity), while storage at
20°C over several months exhibited
minimal activity loss.

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FIG. 1.
SDS-PAGE of fractions from the purification of
Sg-x-PDPP and the autoradiography of the purified peptidase. Lane
1, 15 µg of molecular mass markers (phosphorylase B, 94 kDa; bovine serum albumin, 67 kDa; ovalbumin, 43 kDa; carbonic
anhydrase, 30 kDa; soybean trypsin inhibitor, 20 kDa). The
following lanes contained boiled, reduced samples: lane 2, 140 µg of
80% ammonium sulfate precipitate; lane 3, 102 µg of eluted peak from
DE52 anion exchange; lane 4, 98 µg of peak from Superdex 75 gel
filtration wash; lane 5, 55 µg of eluted peak from phenyl Sepharose;
lane 6, 39 µg of eluted peak from Mono Q anion exchange; lane 7, 15 µg of CB Sepharose flow-through; lane 8, 6 µg of purified
Sg-xPDPP from Gly-Pro Sepharose; lane 9, autoradiograph of
[3H]DFP-labeled enzyme exposed for 96 h to X-ray
film.
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Enzyme specificity
Of the 14 chromogenic endo-
and aminopeptidase substrates tested on purified enzyme (Table
2), only three
(H-Gly-Pro-pNa, H-Ala-Pro-pNa, and
H-Arg-Pro-pNa) were rapidly hydrolyzed. Weaker activity
(<10%) was detected against H-Ala-Ala-pNa. A maximum rate of hydrolysis occurred against H-Gly-Pro-pNa, and Michaelis-Menten kinetics were measured using this substrate. A
Vm of 15.2 µmol min
1
and a Km of 378 µM were observed
with 2 nM of enzyme.
To obtain further information on cleavage specificity, various peptides
were tested as substrates for Sg-xPDPP (Table
3).
Proteolysis was confirmed on peptides
between 4 to 17 residues,
with a proline residue in the
P
1 position. A major impediment
for cleavage was
the presence of Pro in P
1'. There were no
additional
restrictions for amino acids present in the
P
2 and P
1' sites.
The
general formula for proteolysis was deduced as
NH
2-Xaa-Pro(Ala)-

-Yaa-(Xaa)
n,
where Yaa could represent any residue except Pro, Xaa could
represent
any amino acid, and
n represents nonquantified Xaa
residues C
terminal of the Yaa residue. The combined data for synthetic
and
peptide substrates fit a profile that was consistent with previous
data for gram-positive bacterial x-prolyl DPPs (
11,
20,
21,
28,
33,
34,
36) and gram-negative DPPIV families (
2,
56). Extended-time incubation with peptides failed to yield
additional peptide fragments, indicating the absence of endopeptidase
activity or contaminating aminopeptidases. Proteolysis of CC chemokines
(RANTES and MIP-1

), which presented an unblocked x-prolyl N
terminus,
was not observed under identical conditions as peptide
substrates.
The inability of Sg-xPDPP to catalyze endospecific
proteolysis
was tested on whole protein substrates (azocasein, gelatin,
collagen
type IV, and fibrinogen). Internal digestion was not observed
after standard incubations and SDS-PAGE analysis (data not shown).
Inhibition and activation studies.
Autoradiography of purified
Sg-xPDPP radiolabeled with [1,3-3H]DFP (Fig. 1,
lane 9) positively identified the protease as a member of the serine
class. Further studies with class-specific inhibitors (Table
4) supported this assignment. Sensitivity
to serine protease inhibitors (Pefabloc, PMSF, and
3,4-dichloroisocoumarin) was observed, while cysteine class
(iodoacetamide and E64) and metallo class (EDTA and
1,10-orthophenanthroline) members had little or no effect on
activity. Compounds specific for aminopeptidase B and leucine
aminopeptidase (bestatin) and aminopeptidase P (apstatin) were not
inhibitory. However, Sg-xPDPP was highly sensitive to the
DPPIV/CD26-specific inhibitors, H-Glu-pyrollidide and diprotin A
(Ile-Pro-Ile), as evidenced by 50% inhibitory concentration values of
approximately 100 µM. Human plasma inhibitors,
-1-proteinase inhibitor and
-2-macroglobulin, had no effect on enzymatic
activity. Sg-xPDPP activity was also inhibited by the heavy metal
ions Zn2+ and Co2+ at 0.5 and 5 mM, respectively. Complete inactivation occurred in the presence
of 1% SDS detergent. Activity was unaffected by reducing
agents and urea. Gly-Pro-Arg-Pro-amide served as a competitive inhibitor, while the dipeptide, Gly-Pro, provided no inhibition. In
contrast, Gly-Gly moderately stimulated pNa hydrolysis.
Sg-xPDPP sequence analysis and gene structure.
N-terminal and
internal sequences facilitated the construction of degenerate primers.
PCR against an FSS2 library resulted in the isolation of a 960-bp
fragment that represented the N terminus of the protein. This product
was used to search the genomic clone of a relatively uncharacterized
S. gordonii strain in the Unfinished Microbial Genomes
database of TIGR. An ORF of 2,280 bp was identified and was found to
correspond to Sg-xPDPP on the basis of the conservation of
protein-derived peptides. Primers were designed from the electronic sequence, and a PCR approach was used to obtain a full-length DNA
fragment encoding DPPIV. A 759-amino-acid polypeptide with a
theoretical molecular mass of 87,115 Da and a calculated pI of 5.6 was
encoded by this ORF. This is in agreement with the observed
experimental mass, while the native-state dimer is produced by
association of two identical monomers. There is no evidence for
posttranslational modifications of the gene product. The homology search (Fig. 2) performed using the
National Center for Biotechnology Information TBLASTN tool
against EMBL, DDBJ, GenBank, and PDB databases indicated that Sg-xPDPP
is a new member of the x-prolyl DPP S15 family grouped in the SC clan
of serine peptidases (5). This family had previously
consisted of peptidases that derive from lactic acid bacteria
(Lactobacillus spp. and Lactococcus spp.), known
as PepX (51). Sg-xPDPP shares the closest homology with
putative genes uncovered in Streptococcus pneumoniae (72% identity) and Streptococcus mutans (57% identity) while
maintaining only 48% and 34% identity with Lactococcus and
Lactobacillus, respectively. Sg-xPDPP displays evolutionary
divergence from bacterial members of the DPPIV (S9) family,
Flavobacterium meningosepticum (10% identity), and
Porphyromonas gingivalis (11% identity), although it shares
functional similarities. The active-site serine has been identified in
the PepX gene of L. lactis as Ser348 inside the motif GKSYLG
(6). Thus, by analogy Ser347 of Sg-xPDPP is likely to be
the active-site residue. Streptococcal xPDPPs and PepX have nearly
identical residues flanking the catalytic motif, except for a
hydrophobic amino acid replacing a charged Lys in the second position.
Based upon homology to SC peptidases with Ser-Asp-His active-site
nomenclature, Asp574 and Asp576 and His733 of Sg-xPDPP are likely
candidates for the catalytic triad (44). A
computer-assisted search for protein localization predicted neither
signal sequence sites nor transmembrane regions in the protein
(37). Although lacking an export signal and predicted to
be cytoplasmic, activity detected on the cell surface and within supernatant revealed 20% of activity to be extracellular.

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FIG. 2.
Multiple sequence alignment of Sg-xPDPP, putative
streptococcal PepX genes, and other bacterial homologues.
Sequences of Sg-xPDPP (Sgord) deduced from FSS2 genome, putative
x-PDPPs from gene products of S. pneumoniae (Spneu) and
S. mutans (Smut), cloned x-PDPP from Lactococcus
lactis subsp. lactis 763 (Llac763), Lactococcus
lactis subsp. cremoris (Lcrem), Lactobacillus
delbrueckii subsp. lactis (Ldel17290), and cloned DPPIV
from Flavobacterium meningosepticum (Fmenin) and
Porphyromonas gingivalis (Pging) were aligned using the
ClustalW multiple sequence alignment tool according to homology
modeling (grey boxes indicate similarity and black boxes indicate
identity). The putative catalytic residues (serine, aspartic acid, and
histidine) are denoted with asterisks. The arrow marks a consensus
motif flanking the active-site serine in members of the x-PDPP family
(PepX). Double lines represent N-terminal and internal fragments used
to generate a 965-bp PCR product.
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Southern blot analysis revealed Sg-xPDPP to be a single-copy gene (data
not shown). The 2.3-kb ORF was examined in the electronic
database for
the presence of promoter elements and additional
genes. Three ORFs were
revealed and designated ORF 1 (760 codons),
ORF 2 (277 codons), and ORF
3 (236 codons). Sg-xPDPP is coded
by ORF 1, while ORFs 2 and 3 are
oriented upstream on complementary
strands in reverse directions. A
ribosome binding site was identified
5 bp upstream of the start codon.
The putative transcription start
site was found 33 bp from the start
Met as well as the TATA (

10
box) and

35 region promoters. ORF 2 is
118 bp upstream from the
start codon of ORF 1. The protein specified by
ORF 2 has close
to 70% identity with a hypothetical 30.9-kDa protein
found in
the PepX 5' region of
L. lactis (
31,
38) and shares significant
homology to the glycerol uptake
facilitator (Glpf) from
S. pneumoniae (
47). ORF
3 is 1,091 bp upstream from ORF 1 and encodes a 236-amino-acid
protein
with no significant homology to proteins in the aforementioned
databases.
 |
DISCUSSION |
This report describes the purification, characterization, cloning,
and sequence analysis of an extracellular x-prolyl DPP from S. gordonii FSS2. This activity has been described in studies concerning tripeptide degradation systems of S. sanguinis
and S. mutans (8) and collagen degradation by
S. gordonii Challis in the IE model (19). Our
work presents the first biochemical and genetic studies of purified
enzyme. Filtrate obtained from a pH-controlled culture of S. gordonii FSS2 enabled the purification of Sg-xPDPP by more than
6,000-fold. The preparation was determined to be homogenous and
consisted of two identical, noncovalently attached monomers in the
native state. Inactivation studies revealed a serine class catalytic
mechanism in which DPPIV family inhibitors appear to be the most
effective. Specificity studies were conducted using paranitroanalides
and peptides smaller than 20 residues. Limited proteolysis was observed
upon incubation with either substrate. The requirement of Pro or Ala in
the penultimate position and prohibition of Pro in the P1' site define
the specific nature of this peptidase.
Collectively, the biochemical data are consistent with studies on
DPPIV-like peptidases from S. mitis (11),
Streptococcus thermophilus (33), and
Streptococcus salivarius (35). Comparison of
the Sg-xPDPP protein sequence with that of cloned x-prolyl DPPs reveals
significant homology (41% average identity) with PepX gene products of
lactic acid bacteria (31, 34). Putative genes for x-prolyl
DPP were identified in unfinished microbial genomes for S. mutans and S. pneumoniae and maintained 57% and 72%
identity to Sg-xPDPP, respectively. The consensus sequence, GXSYLG, is
present at the active site of PepX and streptococcal members.
Phylogenetically related viridans members, S. pneumoniae and S. gordonii, maintain hydrophobic
residues at the second position which are contrasts to basic residues
conserved in other species. The PepX gene and streptococcal analogue
appear to have diverged from a common ancestor that bears little
sequence homology to the DPPIV/CD26 family of eukaryotic and
gram-negative peptidases. Sg-xPDPP closely resembles members of the S15
family (EC 3.4.14.11), yet our discovery of streptococcal members
with remarkable evolutionary conservation may warrant a
change in nomenclature.
The localization of peptidases outside of the cell is considered to be
a necessary mechanism for the degradation and intracellular transport
of endopeptidase-liberated peptides. Currently, all reported x-prolyl
DPP members from gram-positive bacteria have been associated either
with cytoplasmic membrane or with whole-cell extracts
(24). Sg-xPDPP represents the first peptidase from this
group isolated from an extracellular source. Sequence analysis did not
reveal an N-terminal signal sequence, LPXTG motif (39), or
posttranslational modifications that could account for translocation from the cytoplasm. We found the gene for Sg-xPDPP to be single copy,
ruling out the possibility of an altered form of the peptidase. Previous reports have suggested that such enigmatic transport is the
result of specific leakage of cytoplasmic aminopeptidase from cells
(51) or the shedding of protease-peptidoglycan complexes as a consequence of cell wall turnover (19). In S. gordonii G9B, extracellular protein profiles were altered by
changes in pH, growth medium composition, and rate of growth
(23). Additionally, the secretion of two cytoplasmic
proteins from S. gordonii, a GAPDH (40) and
collagenase (19), was observed upon growth at a constant,
neutral pH. In studies conducted by Harty et al., specific activities
of extracellular proteases (thrombin-like, Hageman factor, and
collagenase) from FSS2 increased severalfold upon a shift in pH from
6.5 to 7.5 (13).These data are consistent with maximum
detection of our Sg-xPDPP activity at a controlled pH of 7.5. Furthermore, the peak of Gly-Pro-pNa activity occurred during early stationary phase, when excess glucose had been exhausted. The alkaline environment of the buffered vegetation that contacts the
bloodstream may be more suitable for enzyme release from the cell. An
extracellular peptidase would therefore better serve the nutritional
requirements of the bacteria in fibrin and/or extracellular
matrix surroundings versus the carbohydrate-rich oral environment.
The biological significance of Sg-xPDPP outside of the cell would serve
a threefold purpose: (i) the production of proline-containing dipeptides that could subsequently be transported into the cell, (ii) a
synergy with other secreted proteases that would permit the degradation
of host proteins, and (iii) the modification of bioactive peptides at
the endothelium. L. lactis and other lactic acid bacteria
are unable to import free Pro, which must be transported in a
peptide-bound configuration (24). A tripeptide transport system was identified in S. sanguinis that permitted the
assimilation of free amino acids by membrane-bound and intracellular
proteolysis. It was further concluded that x-prolyl dipeptides were
insufficient for transport (8). This is counterintuitive
to the action of Sg-xPDPP that results in high concentrations of
extracellular dipeptides. In S. gordonii, uptake could be
driven by an inwardly directed chemical gradient maintained by
fluctuating levels of extracellular and cell-associated products of
peptide hydrolysis. The limited cleavage specificity of Sg-xPDPP
prohibits the independent proteolysis of constituents within and
surrounding the thrombotic vegetation.
Neither type IV collagen nor fibrin(ogen) was a suitable substrate for
the enzyme. This contrasts with the finding of Juarez and Stinson of a
Gly-Pro-pNa activity capable of endopeptidase attack on
native collagen (19). Culture supernatant of FSS2 yielded
several endopeptidase activities capable of degrading denatured
collagen, fibrinogen, and azocasein. Two additional extracellular
aminopeptidases, an Arg-specific aminopeptidase and PepV tripeptidase
(J. M. Goldstein et al., unpublished data), would participate in
the acquisition of small peptides from the protein meshwork surrounding
the bacteria.
Although Sg-xPDPP achieved proteolysis of all suitable peptides tested,
there is an apparent restriction of substrate size. Three cytokines
tested (RANTES, MIP-1
, and granulocyte-macrophage colony-stimulating
factor), presenting unblocked x-prolyl motifs, failed to undergo
cleavage upon extended incubations and increased enzyme/substrate molar ratios. This is in contrast to the
activities of DPPIV/CD26 members which facilitate the N-terminal
proteolysis of these larger substrates despite their high catalytic
similarity to the PepX members (16, 43). Sequence
divergence in specificity pockets and the presence of adhesion domains,
absent in gram-positive peptidases, may contribute to this phenomenon.
The removal of two dipeptides from substance P was observed, and this
heptapeptide product has been found to display biological activity more
potent than that of the intact peptide (55). Additionally,
the concerted action of an extracellular Arg aminopeptidase and
Sg-xPDPP produces a truncated form of bradykinin that has lost
essential residues for receptor activation (3). The
combined effect of these modifications may result in local changes in
vascular permeability and smooth muscle contraction at the infected
endothelium. The truncation of fibrin inhibitory peptides by Sg-xPDPP
could have consequences on thrombus formation and the overall
growth of the vegetation. The soluble tetrapeptide (GPRP),
representing the N terminus of the fibrin
-chain, blocks the
polymerization of fibrin monomers, leading to blocked polymerization,
decreased clotting, and increased clotting times
(27). The minimum structural unit (GPR) is required for inhibitory action. Sg-xPDPP may inactivate circulating inhibitor in
the growing thrombus and alter the balance between polymerization and
fibrinolysis in favor of a growing vegetation. Future studies will
focus on the expression and knockout of Sg-xPDPP in order to evaluate
its relative contributions to streptococcal virulence and survival at
the site of infection.
 |
ACKNOWLEDGMENTS |
This work was supported by National Institutes of Health grant
DE-097621.
We thank TIGR for utilization of the unfinished database.
 |
FOOTNOTES |
*
Corresponding author. Mailing address: Department of
Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229. Phone: (706) 542-1713. Fax: (706) 542-3719. E-mail: jtravis{at}arches.uga.edu.
Editor:
D. L. Burns
 |
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Infection and Immunity, September 2001, p. 5494-5501, Vol. 69, No. 9
0019-9567/01/$04.00+0 DOI: 10.1128/IAI.69.9.5494-5501.2001
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