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Journal of Bacteriology, November 2002, p. 6316-6324, Vol. 184, No. 22
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.22.6316-6324.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana,1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas,2 Department of Microbiology, Mount Sinai Hospital and University of Toronto, Toronto, Canada,3 Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah4
Received 22 April 2002/ Accepted 11 June 2002
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Comparative genomics, proteomics, DNA microarray analysis, and other postgenomic strategies have provided many new avenues for investigating differences in pathogen phenotype, host specificity, and virulence determinants. Genes encoding proteins likely to be extracellular or displayed on the bacterial cell surface can now be identified by analysis of the genome sequence of the pathogen, facilitating rapid discovery of proteins that may interact with the host during natural infection (14, 21, 32). Analysis of genome sequence data can also assist identification of proteins that may confer protective immunity against infection. For example, Pizza et al. (35) analyzed the genome sequence of a serogroup B Neisseria meningitidis strain and identified 570 open reading frames (ORFs) that were predicted to encode novel exported or surface-exposed proteins. The ORFs were cloned, and recombinant proteins were purified and used for immunologic studies. Seven proteins generated an antibody response that conferred complement-mediated bactericidal activity in a murine model of infection. Molecular population genetic analysis indicated that five of the seven proteins were conserved among 31 N. meningitidis strains representative of the species diversity found in natural populations. Taken together, the results have stimulated additional research into the utility of using these proteins as a meningococcal vaccine.
Analysis of the genomes of four GAS strains (serotypes M1, M3, M5, and M18) recently led to the discovery of four genes (spy0747, spy0843, spy0872, and spy1972) that encode novel extracellular proteins (Table 1) (37). The four proteins have conventional amino-terminal secretion signal sequences and have a carboxy-terminal LPXTG amino acid motif that covalently links many gram-positive bacterial virulence factors to the bacterial cell surface (13, 34, 37, 39). Sequencing and population genetic analysis of these four GAS genes in 37 strains revealed restricted allelic variation, indicating that the proteins are very well conserved in the species (37). Western immunoblot analysis conducted with acute- and convalescent-phase serum samples obtained from four patients with invasive infections indicated that all four of the recombinant proteins were reactive with one or more of the serum samples, consistent with the hypothesis that these proteins are produced during GAS infections (37). Taken together, these preliminary observations suggest that further analysis of these proteins is warranted.
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TABLE 1. Chromosomal location and putative function of four GAS genes
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DNA sequence analysis. Chromosomal DNA was isolated with the Puregene DNA Isolation kit (Gentra Systems). DNA sequencing primers were designed on the basis of M1, M3, and M18 genome data (11) (Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health). Sequence data obtained from both DNA strands with an Applied Biosystems 3700 automated sequencer were assembled with DNAStar (DNAStar, Inc.). Multiple-sequence alignment of the inferred amino acid sequences was performed with CLUSTALW (version 1.8) (42), and analysis of sequence polymorphisms was performed with MEGA 2.1 (http://www.megasoftware.net/).
Gene cloning and expression of recombinant GST fusion proteins.
Cloning primers were designed on the basis of M1 genome data (11), and MGAS5005 (serotype M1) was used as the source strain for DNA. Full-length genes, minus the region encoding the putative signal secretion sequence, were cloned with the Univector plasmid fusion system (UPS) (26). The method employs bacteriophage P1 cre-lox site-specific recombination to catalyze in vitro plasmid fusion between the Univector containing the gene of interest, and a host vector (pHB2-GST) containing a GST tag (26). Briefly, each gene was cloned into the pUNI-D vector in the same frame as the loxP site using vaccinia virus topoisomerase I-based cloning (40). For these experiments, the pUNI-D vector adapted with topoisomerase I was obtained from Invitrogen, Inc., and PCR products of the genes of interest were inserted into the plasmid according to the manufacturer's instructions. The pUNI-D clones were converted to glutathione S-transferase (GST) fusions by combining 0.4 µg of the pUNI-D clone with pHB2-GST DNA in 20 µl of 1x buffer S (50 mM Tris-Cl [pH 7.5], 10 mM MgCl2, 30 mM NaCl, and 0.1 mg of bovine serum albumin per ml) on ice. Immediately after addition of 0.1 to 0.2 µg of GST-Cre enzyme, the reaction mixture was incubated at 37°C for 20 min followed by 5 min at 65°C to inactivate the GST-Cre enzyme. Recombination products of the UPS were selected on Luria-Bertani agar containing 50 µg of kanamycin per ml after transformation of Escherichia coli DH5
by standard methods. Clones were sequenced to rule out the possibility of spurious mutations. To assess protein production, recombinant E. coli DH5
strains were grown at 37°C in 10 ml of Luria-Bertani broth supplemented with 50 µg of kanamycin per ml. Cultures were induced at an A600 of 0.5 with 0.2 to 0.5 mM isopropyl-ß-D-thiogalactopyranoside (IPTG) and grown overnight at 25°C. Cells were pelleted by centrifugation, lysed, and analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE).
Western immunoblot analysis. A 1:20 dilution of each E. coli lysate containing recombinant protein was analyzed by SDS-PAGE, transferred to a nitrocellulose membrane (Millipore), and probed with patient sera. The sera studied included the following: convalescent-phase serum samples collected from 9 patients with pharyngitis, paired acute- and convalescent-phase serum samples obtained from 27 patients with invasive GAS infections, paired acute- and convalescent-phase serum samples collected from four patients with superficial skin infections, and convalescent-phase serum samples obtained from 40 patients with a history of ARF. Convalescent-phase sera were collected approximately 3 weeks postinfection. In some cases, sera obtained from patients with a history of ARF were collected several years after the last documented presentation with ARF symptoms.
Recombinant proteins were transferred with a Bio-Rad semidry transfer chamber (Bio-Rad Laboratories) for 60 min at 15 V. Following transfer, the membrane was treated with a 5% (wt/vol) solution of dehydrated milk in blocking buffer (100 mM Tris-HCl [pH 7.4] and 150 mM NaCl) for 1 h. Primary antibody (patient serum) was added to the blocking reagent, and the membrane was incubated for 1 h. The patient sera was used at a dilution of either 1:500 or 1:1,000, depending on serologic reactivity. Goat anti-human affinity-purified immunoglobulin G (IgG) (Bio-Rad) was used as the secondary antibody. Signal detection was conducted with SuperSignal West Pico chemiluminescent substrate (Pierce).
TaqMan real-time reverse transcriptase PCR analysis. Cultures of representative GAS serotype M1 (MGAS5005), serotype M3 (MGAS315), and serotype M18 (MGAS8232) strains were grown in THY medium (37) overnight at 37°C (5% CO2). A 100-µl aliquot of each culture was added to 50 ml of THY medium, incubated at 37°C (5% CO2), and harvested at six time points (A600 = 0.05, 0.1, 0.2, 0.4, 0.6, and 0.8) throughout the growth cycle (see Fig. 2). Total RNA was isolated at each time point as previously described (4).
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FIG. 2. Fold increase in gene transcript levels assessed by TaqMan assays at six time points throughout the growth cycle. Cultures of representative group A Streptococcus serotype M1 (MGAS5005), serotype M3 (MGAS315), and serotype M18 (MGAS8232) strains grown overnight were diluted 1:500 in 50 ml of THY medium, incubated at 37°C (5% CO2), and harvested at six time points (A600 = 0.05, 0.1, 0.2, 0.4, 0.6, and 0.8) throughout the growth cycle. cDNA prepared from strains of serotype M1 (MGAS5005), M3 (MGAS315), and M18 (MGAS8232) was measured for transcripts of spy0747 (putative extracellular nuclease), spy0843 (putative cell surface protein), spy0872 (putative 2',3'-cyclic-nucleotide 2'-phosphodiesterase), and spy1972 (putative pullulanase). All measurements were normalized to the gyrA transcript as described in Materials and Methods. Values are expressed as the fold increase in transcript compared to the transcript level at an A600 of 0.05. The data represent values obtained with at least two independently isolated RNA samples analyzed in triplicate.
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Purification of recombinant Spy0843 and Spy1972. Purified recombinant Spy0843 and Spy1972 were obtained with the B-PER GST Fusion Protein Purification Kit (Pierce) with slight modifications. One milliliter of resin was used for every 100 ml of bacterial culture. Benzonuclease (1 µl) (Novagen) was added for every ml of B-PER Reagent used to resuspend the cell pellet, and phenylmethylsulfonyl fluoride was added to a final concentration of 25 mM.
Affinity-purified anti-Spy0843 and anti-Spy1972 antibodies. Purified recombinant Spy0843 and Spy1972 were supplied to Bethyl Laboratories for producing purified antibodies. Rabbits were immunized or given booster doses of 100 µg of antigen every 2 weeks for 2 months and then immunized or given booster doses once a month. The first immunization contained antigen and complete Freund's adjuvant at a 1:1 ratio. All subsequent immunizations contained antigen and incomplete Freund's adjuvant at a 1:1 ratio. The animals were bled every 2 weeks after the third immunization (5 weeks). Hyperimmune serum samples from rabbits were processed over a GST column to absorb anti-GST antibodies. The serum was then passed over an immunosorbent (Spy0843 or Spy1972 peptide linked to agarose using a cyanogen bromide method) to capture antibodies specific for the protein. Antibodies were filtered in a sterile manner and supplied in a neutral buffer with sodium azide (0.1%) as an antimicrobial agent.
Expression of Spy0843 and Spy1972 on the GAS cell surface. Surface expression of Spy0843 and Spy1972 was analyzed with a FACScaliber flow cytometer (Becton Dickinson) using the affinity-purified Spy0843- and Spy1972-specific antibodies. Purified rabbit IgG raised against an irrelevant protein antigen was used as a control for nonspecific antibody binding. Briefly, GAS strain MGAS5005 (serotype M1) was grown to late exponential phase (A600 = 0.7) in THY medium, harvested by centrifugation, washed twice in Dulbeccos phosphate-buffered saline (DPBS) (pH 7.2), and resuspended in DPBS at 108 CFU/ml. Anti-Spy1972 and anti-Spy0843 antibodies were added to 100 µl of bacterial suspension at a final concentration of 1 µg/100 µl and incubated for 30 min on ice. Samples were washed with DPBS containing 1% goat serum and stained with phycoerythrin-conjugated donkey anti-rabbit IgG (Jackson ImmunoResearch) (1:400 dilution) for 30 min on ice prior to flow cytometry.
Active immunization of mice with purified Spy0843 and Spy1972. Four groups of 25 female Swiss CD-1 outbred mice were inoculated with either PBS or 5, 10, or 20 µg of Spy0843 or Spy1972 in PBS subcutaneously on day 1. Booster doses of the same treatments were administered on days 14 and 28. The adjuvant monophosphoryl lipid A (Corixa, Hamilton, Mont.) was added to all doses. Mice were challenged intraperitoneally with 1.82 x 108 CFU (0.2 ml) of strain MGAS5005 (serotype M1) on day 35. Bacteria were harvested when maximal transcription of the gene encoding the protein of interest was reached as indicated by TaqMan assays (see Results). The number of CFU inoculated per mouse was verified by colony counts. Mice were monitored every 3 h for 7 days, mortality was recorded, and Kaplan-Meier survival curves were plotted (JMP statistical software). The Wilcoxon test was used to test for statistical differences in survival.
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Reactivity of human sera with recombinant proteins. A recent study suggested that the four proteins investigated here were produced in humans infected with GAS (37). The preliminary study was limited to the Western immunoblot analysis of sera collected from seven healthy individuals and four patients with invasive GAS infections. Hence, it is not known if antibodies specific for each protein are generated in response to several distinct infection types. To investigate this issue, Western immunoblot analysis was conducted with paired acute- and convalescent-phase serum samples collected from 27 patients with invasive GAS infections (culture positive from a normally sterile site) and from 4 patients with superficial skin infections (noninvasive) (Table 2). The infecting strains represented 19 distinct M protein serotypes (Table 2).
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TABLE 2. Reactivity of four recombinant GAS proteins with human convalescent sera obtained from patients with GAS disease
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Each of the proteins reacted with
19.4% of the acute-phase serum samples (n = 31) isolated from patients with invasive disease (data not shown). This is not unexpected, given the variation in the length of time from the onset of infection to the time the patient seeks treatment. Importantly, when reactivity with acute-phase sera was observed, the reactivity of the convalescent-phase serum sample was far more intense, a result consistent with recent exposure to a given protein (Fig. 1).
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FIG. 1. Western immunoblot showing typical reactivity of paired acute- and convalescent-phase serum samples with purified recombinant proteins. Acute-phase serum was collected when a patient first sought treatment. Convalescent-phase serum was collected approximately 3 weeks postinfection. The immunoblot is representative of results obtained for each of the four group A Streptococcus proteins (reactivity with Spy1972 is shown). A 1:20 dilution of E. coli lysate containing recombinant Spy1972 and a 1:500 dilution of patient serum was used. Lane 1, molecular mass markers; lane 2, reactive acute-phase serum sample; lane 3, reactive, convalescent-phase serum. The increased reactivity with the convalescent-phase serum sample is consistent with recent exposure to Spy1972.
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85% of individuals with ARF. Spy0872 was far less reactive (<25% with sera from individuals with pharyngitis or ARF) (Table 3). |
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TABLE 3. Immunoreactivity of recombinant GAS proteins with human sera obtained from patients with GAS infections
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Second, the level of gene transcript also varied among the three strains. For example, the transcript level of spy0843 in the M3 strain was higher than the M1 or M18 strain at all but the earliest time point (A600 = 0.05). Similarly, the transcript level of spy0872 was very similar at each time point until stationary phase (A600 = 0.8), at which point the transcript level in the M1 strain increased > 2.5-fold and the transcript levels in the M3 and M18 strains decreased (Fig. 2). Transcript levels of all three alleles of spy1972 were low until A600 = 0.6 when the transcript level increased
35-fold (Fig. 2). Interestingly, the transcript level of spy1972 in the M1 strain remained greatly elevated at A600 = 0.8, whereas the transcript level of the alleles in the M3 and M18 strains decreased to near-initial levels.
Purification of recombinant Spy0843 and Spy1972. Spy0843 and Spy1972 were overexpressed in soluble form in E. coli BL21(DE3) and purified to apparent homogeneity (Fig. 3). Amino-terminal amino acid sequencing confirmed the identity of each protein (data not shown). We were unable to purify Spy0747 because the recombinant protein was insoluble. The subsequent purification of Spy0872 was not pursued due to the lack of seroreactivity with the majority of serum samples examined and the apparent low level of protein expression throughout growth in three GAS serotypes.
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FIG. 3. SDS-PAGE showing purified recombinant Spy1972 and Spy0843 (recombinant Spy1972 and Spy0843 are GST fusion proteins). The gel was stained with Coomassie brilliant blue. Lane 1, molecular mass marker; lane 2, purified recombinant Spy1972; lane 3, purified recombinant Spy0843.
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Detection of Spy0843 and Spy1972 on the surface of GAS. The presence of Spy0843 and Spy1972 on the surface of live GAS was confirmed by flow cytometry (Fig. 4). The ability of purified anti-Spy0843 and anti-Spy1972 antibodies to bind to GAS was demonstrated by increased fluorescence compared to that with control antibody (Fig. 4). Each antibody recognized its respective antigen on the surface of GAS, as demonstrated by a substantial shift in fluorescence over control antibody (Fig. 4). Western immunoblot analysis confirmed that the respective antibodies were not cross-reactive (data not shown).
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FIG. 4. Detection of Spy0843 (A) and Spy1972 (B) on the GAS cell surface by flow cytometry. Control antibody (unshaded histograms) and purified anti-Spy0843 and anti-Spy1972 (shaded histograms) were incubated with strain MGAS5005 (serotype M1) and analyzed by flow cytometry. The unshaded histograms represent the level of nonspecific binding of the control antibody to MGAS5005. The shaded histograms indicate increased fluorescence due to the binding of anti-Spy0843 or anti-Spy1972 antibody to the MGAS5005 cell surface.
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A common strategy used to identify proteins for vaccine-related research is to select antigens on the basis of immunologic data obtained from patients with diverse infection types (14). One important limitation of our initial study (37) was that only four serum samples obtained from patients with invasive disease were examined. Inasmuch as the complement of proteins made during various types of GAS infections (pharyngitis, cellulitis, necrotizing fasciitis, etc.) may differ, we sought evidence that each protein was produced in many patients with multiple infection types. Western immunoblot analysis confirmed that all four proteins (Spy0747, Spy0843, Spy 0872, and Spy1972) are made during the course of distinct GAS infections. This result suggests that if antibodies against one or more of the proteins contribute to protection against infection, protection may extend to different GAS infection types.
The frequency of reactivity of Spy0872 with sera isolated from human patients was considerably less than those of the other three proteins. However, all serum samples obtained from patients infected by a serotype M1 organism were reactive with recombinant Spy0872 (Table 2). Consistent with the serologic data, only the serotype M1 strain had an increase in the level of spy0872 transcript throughout the growth cycle (Fig. 2). Thus, the low level of serologic reactivity may be due to relatively minimal transcription of the spy0872 gene by non-M1 serotypes. This is an important new finding. Spy0872 may not be suitable for further vaccine-related studies due to a lack of seroreactivity with the majority of serum samples examined and the apparent low level of protein expression throughout growth in three GAS serotypes (Tables 2 and 3 and Fig. 2).
For unknown reasons, serotype M1 organisms cause many more GAS infections than the other serotypes do (33). One observation of note is that only serum samples obtained from patients infected with a serotype M1 organism consistently had antibodies to all four proteins. Very low levels of amino acid variation in all four proteins argue against the possibility that the absence of serologic reactivity with these proteins was caused by strain-specific variation in amino acid sequence. In contrast, TaqMan assay results clearly indicated that the levels of transcripts produced can vary by serotype. It is possible that decreased levels of transcription by some strains led to very low levels of protein synthesis and antibody production, and hence, lack of reactivity in the Western immunoblot analysis. Perhaps M1 organisms are adept at causing infection due to higher levels of gene transcription and virulence factor production, on average, than those of many other GAS strains.
TaqMan analysis has proved to be a very rapid method of gaining insight into GAS gene regulation (4, 37, 41). Analysis of isogenic mutant strains by TaqMan assays (37) has implicated the GAS virulence gene regulators covR (negative regulator of several GAS virulence factors, including cysteine protease and capsule) (10, 25) and mga (positive regulator of M protein, C5a peptidase, streptococcal inhibitor of complement, and streptococcal collagen-like protein 1) (27, 29, 30) in the control of expression of several of the genes studied here. For example, transcription of spy0747 and spy0843 was up regulated in the absence of the CovR repressor, whereas expression of spy1972 was down regulated in the absence of the positive regulator encoded by mga (37). In contrast, a recent microarray and TaqMan analysis of differential gene expression in response to alteration in growth temperature did not implicate temperature in the regulation of these four genes (41). It will be important in future studies to analyze the pattern of gene transcription in experimentally infected animals and human patients with naturally acquired disease.
Several recent studies have suggested that postgenomic strategies to triage the analysis of protein vaccine candidates identified by comparative genomics could benefit by taking into consideration the degree of amino acid conservation (1, 35, 37, 38, 43). Use of an antigen that is conserved among all or most strains of a species is likely to reduce the possibility of variability in serologic reactivity, and subsequent immunologic protection, due to strain-specific differences in protein sequence. The same line of reasoning applies to gene transcription. Our studies indicate that the maximal transcript level and the time of maximal expression differed among the four genes for each of the three strains (serotypes M1, M3, and M18) examined. This implies that although a protein may be conserved and capable of interacting with the host during infection, variation in the level and timing of gene expression and subsequent protein synthesis among strains may fundamentally alter the role of the protein in host-pathogen interactions. An integrated strategy for identifying new vaccine candidates that incorporates analysis of variation in gene transcription (TaqMan analysis) and amino acid composition (comparative sequencing) may assist identification of constitutively expressed genes which encode highly conserved protein antigens that stimulate a relatively consistent immunologic response in the host. Moreover, this approach would likely identify strains that have significant variation in gene transcription or amino acid composition of the antigen. These strains could be very useful for heterologous challenge studies.
Each of the genes studied encoded a protein with a carboxy-terminal LPXTG cell wall anchor motif. More than 50 extracellular proteins with this motif in gram-positive bacteria have been described, and many of these proteins are virulence factors (12). For example, in GAS this amino acid motif is present in M protein, M-like proteins, C5a peptidase, GRAB protein, serum opacity factor, a fibronectin-binding protein, streptococcal protective antigen, and two collagen-like proteins (5, 8, 12, 27, 28, 36). All of these proteins are known to be accessible on the GAS cell surface. We confirmed that the LPXTG motif-containing proteins Spy0843 and Spy1972 are also displayed on the GAS cell surface. Importantly, all five GAS cell surface proteins with an LPXTG anchor motif or closely related amino acid sequence that have been extensively studied (M protein, C5a peptidase, serum opacity factor, a fibronectin-binding protein, and streptococcal protective antigen) are virulence factors and contribute to protective immunity in mouse models (7, 8, 15, 22). Here we show that immunization with purified recombinant Spy0843 can confer protection against intraperitoneal challenge in a mouse model of GAS infection. This suggests that antibodies specific for Spy0843 may contribute to a protective host immune response. Additional work will be needed to investigate this issue in other models of animal infection.
In summary, our studies provide additional evidence that new therapeutic agent candidates can be identified and characterized rapidly by postgenomic strategies. The results also highlight the advantages of integrating TaqMan transcription analysis with Western immunoblot results to determine if a protein is made in infected hosts and transcribed in strains that express different M-protein serotypes. Analyses of the roles of these four proteins in host-pathogen interactions and of their ability to stimulate protective immunity in animal models may provide new avenues for control of GAS disease.
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2-macroglobulin. J. Biol. Chem. 274:15336-15344.
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