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Infection and Immunity, March 2004, p. 1715-1724, Vol. 72, No. 3
0019-9567/04/$08.00+0 DOI: 10.1128/IAI.72.3.1715-1724.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Departments of Medicine,1 Microbiology, New York University School of Medicine,2 Department of Veterans Affairs Medical Center, New York, New York 100163
Received 5 September 2003/ Returned for modification 24 October 2003/ Accepted 23 November 2003
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As with many other bacterial species (34), C. fetus possesses an outermost crystalline surface layer of regular closely packed high-molecular-weight protein subunits (S-layer proteins [SLPs]) (9, 10, 17, 24, 26). In C. fetus, the SLPs are encoded by five to nine sapA homologues in each strain (11, 18, 40). The C. fetus SLPs have been shown to play a critical role in C. fetus virulence (2, 4, 5, 21, 22, 27) by protecting the bacterium from phagocytosis and serum killing (3). In addition, SLP phase variation results in antigenic variation and thus allows the bacterium to escape from host immune defenses (5, 8, 9, 20, 21).
In wild-type C. fetus subsp. fetus strain 23D, nine (eight complete and one partial) sapA homologues, the unique sap promoter, and the SLP secretion system genes are clustered on a 54-kb chromosomal region termed the sap island, as described previously (41) (Fig. 1). To better understand the conservation and diversity of the C. fetus sap island and to gain further insights into C. fetus antigenic variation mechanisms, we investigated the distribution and profiles of the sapA homologues and the sap island boundaries among C. fetus strains differing in subspecies and serotype. In the course of the present study, we also identified six new sap homologues that further our understanding of sap homologue evolution.
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FIG. 1. Schematic representation and genomic organization of the sap island and its flanking regions in C. fetus strain 23D. For ease of reading, selected ORFs (02, 09, 20, 31, 44, and A to Ap8) representing Cf0002, Cf0009, Cf0020, Cf0031, Cf0044, and sapA to sapAp8, are labeled, respectively. Each arrow represents the ORF orientation.
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TABLE 1. Wild-type C. fetus strains used in this studya
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PCR. Amplifications of the eight sapA homologues in the 18 C. fetus strains were performed by using two sets of homologue-specific primers (Table 2). To detect the presence of Cf0002 and to define the sap island upstream boundaries, PCRs were performed with primer MF paired with MR or paired with AR or BR, respectively (Table 2 and Fig. 2D). The presence of the sap island downstream gene Cf0031 and the sap island downstream boundary were examined by PCRs by using primer DF paired with DR and primer DR paired with AbF or 3F1, respectively (Table 2 and Fig. 3). Cf0009 presence and its location related to sapA homologues were investigated by PCRs with primers HF paired with HR and primer HR paired with AR or BR (Fig. 4A). The Cf0020 and sapC status within the sap island were identified by PCRs with primer TR paired with 2F and with primer CR paired with AR or BR, respectively (Table 2 and Fig. 4E and G). The positions of sapF with sap homologues were examined by using a PCR with primer FF paired with AR or BR (Table 2 and Fig. 4J). Amplifications were performed with 100 ng of chromosomal DNA, 20 pM (each) forward and reverse primers, 350 nM deoxynucleoside triphosphates, 5 µl of the provided buffer, and 0.5 U of Taq polymerase (Qiagen) in a final volume of 50 µl per reaction mixture. PCR conditions consisted of denaturation at 94°C for 1 min, annealing at 5°C below the predicted melting temperature of the primers for 1 min, and extension at 72°C for 1 min kb-1.
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TABLE 2. PCR primers used in this study
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FIG. 2. Identification of the sap island upstream boundary in 18 C. fetus strains. (A) Detection of the presence of Cf0002 (mtfB) by PCR with primers MF and MR. (B) Southern hybridization of Cf0002 with HindIII-digested genomic DNA. The probe is a 707-bp mtfB fragment amplified by PCR from strain 23D. (C) PCR detection of the proximity of Cf0002 to sapA homologues with primers MF and AR (lanes 1 to 11) or primers MF and BR (lanes 12 to 18). (D) Schematic representation of the sap island upstream boundary and the strain 85-388 insertion site and sequence. The black box represents the 5' conserved regions of the sapA or sapB homologues. The PCR primers and orientations are designated by arrows. (E) PCR amplification of the insertion fragment found between Cf0002 and sapA homologue in strain 85-388 with primers IF and IR.
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FIG. 3. Identification of the sap island downstream boundary. (A) Strategy for detection of Cf0031 location relative to the sap island. The primers are shown as arrows, and the black area indicates the 5' conserved regions of the sapA or sapB homologues. (B) PCR amplification for Cf0031 in the 18 C. fetus strains with primers DF and DR. (C) PCR identification of the proximity of Cf0031 with sapA or sapB homologues with primers AbF and DR. (D) PCR identification of the proximity of cf0031 with sapA3 with primers 3F1 and DR.
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FIG.4. Analyses of Cf0009, Cf0020, sapC, and sapF locations related to sapA or sapB homologues within the sap island of 18 C. fetus strains. (A) Schematic representation of PCR for Cf0009 analyses, with primers indicated by the arrows; (B) PCR for detection of the presence of Cf0009; (C) Southern hybridization for Cf0009; (D) PCR amplifications for the location of Cf0009 related to the sapA homologues with primer HR paired with AR (for type A strains) or BR (for type B strains); (E) schematic representation of PCR for Cf0020 analysis, with the primers indicated by the arrows; (F) detection of the location of Cf0020 in relation to sapA2 (or sapB2) by PCR with primers 2F and TR; (G) schematic representation of PCR for sapC analysis, with the primers indicated by arrows; (H) PCR for sapC amplification and orientation with primers AR and CR; (I) PCR for sapC analysis with primers BR and CR; (J) schematic representation of PCR for sapF analysis, with the primers indicated by arrows; (K) PCR for sapF amplification and orientation with primers AR or BR and FF.
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Southern hybridization. Chromosomal DNA was digested with HindIII, electrophoresed on a 1% agarose gel, and transferred to a positively charged nylon membrane. The eight sapA homologue-specific, Cf0002-specific, and Cf0009-specific probes were PCR-amplified products labeled by using the Renaissance Chemiluminescence kit (NEN Research Products, Boston, Mass.).
SDS-PAGE and immunoblotting. The sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis and immunoblotting procedures were used as described previously (40). For immunological detection, recombinant SLP proteins were detected by immunoblotting them on 7% SDS-polyacrylamide gels, with polyclonal rabbit serum against the 97-kDa SLP from C. fetus strain 82-40 LP, as described previously (26). The goat anti-rabbit immunoglobulin G alkaline phosphatase conjugate was used as secondary antibody at a 1:1,000 dilution.
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Next, PCRs with primers MF and AR (or BR) indicated that mtfB is located upstream of a sapA homologue in type A strains but, as expected, not in type B strains (Fig. 2C). The product sizes were conserved in all of the type A strains, except for 85-388 and 85-389, in which larger bands were seen, suggesting an insertion in these two strains (Fig. 2C). Sequence analysis of the product from strain 85-388 indicated a 187-bp polymorphic region, with 24 (TTT) trimers beginning 293 bp and ending 107 bp upstream of the nearest sapA homologue (Fig. 2D). A search of GenBank failed to reveal any significant homology to the 187-bp noncoding sequence. The 187-bp insertion fragment present in strain 85-388 appeared only to be present in the other type A reptile strain (85-389), as determined by PCR with primers IF and IR (Fig. 2E).
In strain 23D, the homologue adjacent to mtfB is sapA4. To determine whether this relation is conserved in the other type A strains, we performed PCR with MF and A4R. The result showed that sapA4 is the homologue closest to the boundary in only 4 (including strain 23D) of 11 strains (data not shown).
Downstream boundaries of the sap islands. Since the downstream boundary of the sap island in strain 23D is flanked by Cf0031, we performed PCRs with a Cf0031-specific reverse primer (DR) paired with either its forward specific primer DF or a sapA/B-specific forward primer AbF (Fig. 3A). The results show that Cf0031 is present and is adjacent to the sap island in all 18 strains (Fig. 3B). The PCR with a sapA3-specific primer and Cf0031-specific primer indicate that sapA3 is adjacent to Cf0031 in 10 of the 18 strains (Fig. 3D), a finding consistent with their presence in these strains (see Fig. 5, sapA3-I). These observations indicate that the downstream border of the sap island is conserved, in contrast to the upstream boundary, where the specific homolog present is not conserved.
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FIG. 5. Distribution of eight sapA homologues in 18 C. fetus strains by using two differing sets (I or II) of sap homologue-specific primers (Table 2). The numbers in parentheses indicate the primer locations in the specified genes. The lane numbers representing the strains are the same as in Table 1; lane C represents the no-DNA control.
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Conservation of the sapA homologues among the 18 C. fetus strains. In C. fetus strain 23D, all eight sapA homologues (sapA and sapA1 to sapA7) showed at least a 553-bp 5' conserved region, partially conserved midregions, and substantially divergent 3' regions. To assess the presence and genetic diversity of these eight sapA homologues in the other 17 C. fetus strains, we performed PCR with sap homologue-specific primers located within the divergent 3' regions. All eight sapA homologues are present in six strains (strains 1, 2, 4, 5, 6, and 10), but one or more homologues were absent in the others (Fig. 5). In particular, of the three reptile strains, strains 7 and 8 showed only sapA and sapA7 PCR products, and strain 12 showed only the sapA7 PCR product. For each PCR product, variation only encompassed homologue presence or absence in a strain; there was no size variation. For each homologue, we performed two independent PCRs to determine whether a negative result was due to primer mismatches or to the absence of the homologue. In each case, except for sapA3, sapA4, and sapA7, results were consistent for the two sets of primers; the observed differences could be due to polymorphisms in the primer regions or suggest new close homologues.
Southern hybridizations were performed with one of the sap homologue-specific PCR products as a probe for each homologue (Fig. 6). Most of the sap homologue-specific hybridizations, with the exception of reptile strains 7, 8, and 13, revealed the same size bands, indicating a close genomic relationships across the strains. The hybridizations with the sapA2 and sapA5 probes showed extra bands in some of the type B strains, suggesting the presence of other gene copies or close homologues.
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FIG. 6. Southern analysis of the distribution of eight sap homologues among C. fetus strains. Each lane contains HindIII-digested genomic DNA from the 18 different C. fetus strains, hybridized with each of eight sap homologue-specific probes and amplified by one set of the PCR products from strain 23D shown in Fig. 5. The numbers in parentheses indicate the probe locations within the specified genes.
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97 kDa, whereas the sizes are >111 kDa on the lower branch. Earlier work showed that 97-kDa SLPs had hexagonal crystalline structure, whereas the larger products formed tetragonal crystals (17).
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FIG.7. Sequence and antigenicity of sapA homologues identified in the present study. (A) Schematic representation of the structures of new sapA homologues compared to their closest homologues in strain 23D. The different colors indicate regions of sequence identity, the white boxes represent diverse sequences, and the red outlined box in sapA10 represents a deletion in the (gray) semiconserved region compared to sapA4 and sapB9. (B) Immunoblot of recombinant SLPs probed with polyclonal rabbit antiserum to the 97-kDa SLP of type A strain 84-20LP. The SLPs are encoded by sapA8, sapA12, sapB11, sapA13, sapB9, sapA, and sapA10, respectively. An immunoreactive product was observed in each case, except for sapB11. (C) Phylogenetic tree constructed from the nucleotide sequences of 16 sapA or sapB homologues, including the six new homologues. The tree was constructed by using PAUP 4.0bs neighbor-joining method based on Kimura's two-parameter model distance matrices. The size of the deduced or experimentally determined SLP encoded by the homologue is shown at the left. The major branching perfectly conforms to the dichotomy between 97-kDa SLP (hexagonal) and >97-kDa SLP (tetragonal) in crystalline structure (17).
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Our present studies indicate that all 18 C. fetus sap islands show a consistent downstream boundary adjacent to Cf0031 and that all type A C. fetus sap islands are located downstream of a potential lipopolysaccharide (LPS) locus. Type B strains do not possess mtfB, a finding which is consistent with the compositional differences between type A and type B LPS (25, 48). Our results do not exclude the possibility that sap islands in type B C. fetus strains share a consistent upstream boundary or that they could be located downstream of their LPS locus. In total, these data provide further evidence that the sap island entered the C. fetus genome before the different subspecies and serotypes diverged and that the type A and type B sapA homologue divergence must have occurred after the island had been present. That Cf0009, encoding a putative high-molecular-weight surface protein (41), only exists in the 15 mammalian, but not reptilian, strains suggests that Cf0009 might have entered the C. fetus genome after the divergence between mammalian and reptilian strains, a finding consistent with analyses of G+C content and dinucleotide signatures (42).
The substantial global direct (18.0%) and inverted (16.5%) repeats in the sap island (42) can mediate DNA rearrangement and lead to instability of the island (14, 30, 39, 43, 44). Southern hybridization with the 5' conserved region as a probe showed different profiles among the strains, suggesting that the sap islands are relatively variable (40). That all eight sapA homologues in C. fetus strain 23D can switch sap island position with one another at high (10-1 to 10-2) frequency due to DNA recombination mediated by their conserved 5' noncoding and coding regions is consistent with the plasticity of the sap island (41). The stable existence of sap island internal genes Cf0009, Cf0020, and sapC among the different strains suggests that the island components and boundaries may be conserved, but we cannot exclude the existence of further smaller polymorphisms.
Reptile and mammalian C. fetus isolates have a number of differences that can be shown in phylogenetic studies (40). Of the eight sapA homologues examined, sapA and sapA7 homologues were detected in strains 85-388 and 85-389, but no sapA homologues were detected in strain 85-387 by PCR or by Southern hybridization. However, the sequence analyses of the cloned sapA homologues in strain 85-387 indicate that sapA1 and sapA7 are present. The reasons for these dichotomous results reflect sequence divergence between the sapA homologues in strains 23D and 85-387. The latter sequence failed to be amplified by the PCR or demonstrated by Southern hybridization due to primer mismatching and internal HindIII sites, respectively (data not shown).
C. fetus strains may be either type A or type B based on the LPS structure and SLP type. The finding that sapA and sapB homologues coexist in strain 85-387 confirms our previous study (40) that strain 85-387 is a type A/B chimera. We excluded the possibility that the strain is a mixture of type A and type B strains. If the sample tested reflected a mixture of two different strains, we would find relatively equal numbers of sapA and sapB bands. However, the probe of the 85-387 genome with the sapA and sapB conserved regions showed six sapB bands and only one sapA band (40). These results indicate that 85-387 indeed represents a single strain. SLPs bind specifically to LPS molecules from homologous (type A or B) but not heterologous cells (49). What the LPS type is for this strain and how the different SLPs bind to LPS remains unknown.
In each C. fetus strain, the unique sapA promoter potentially permits transcription of all of the sapA homologues, resulting in the expression of different SLP antigens (13-16, 39, 41). C. fetus antigenic variation involving the C. fetus SLPs has been observed in vivo and in vitro (21, 30, 45, 46). That different C. fetus strains possess new sap homologues and that their encoded SLPs are antigenically cross-reactive with one another indicate an extensive family of related proteins. The phylogenetic analyses showed no greater difference between mammalian and reptile isolates than between two mammalian strains. The SLP encoded by sapB11 in strain 85-387 did not show cross-antigenicity using the polyclonal antibody against the 97-kDa SLP encoded by the sapA homologue in type A C. fetus strain 82-40LP, indicating that they do not share major epitopes. This result suggests that the design of potential C. fetus vaccines should include a pool of different antigens. Finally, the deep branching of the phylogeny of the homologues corresponds exactly to the observed differences in protein size and in crystalline structure (17). These results both confirm the utility of the distinction and suggest that an ancient gene duplication event led to the major branching. That the sapB homologues are present on separate branches suggests recombination events to explain this homoplasy.
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