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Infection and Immunity, December 2008, p. 5668-5676, Vol. 76, No. 12
0019-9567/08/$08.00+0 doi:10.1128/IAI.00930-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Department of Pharmaceutical Sciences, The University of Oklahoma Health Sciences Center, P.O. Box 26901, Oklahoma City, Oklahoma 73126
Received 25 July 2008/ Returned for modification 2 September 2008/ Accepted 19 September 2008
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Members of the AraC/XylS transcriptional regulator family have been characterized from a wide variety of prokaryotes including both gram-negative and gram-positive bacteria. The characteristic feature of this family is a conserved stretch of approximately 100 amino acids at the C-terminal end that serves as the DNA-binding domain (10). Within this domain, two helix-turn-helix motifs are responsible for binding to adjacent major grooves that constitute the DNA-binding site (10). In addition, most members contain a domain responsible for dimerization and interaction with a ligand effector molecule. The main regulatory roles ascribed to this family are carbon metabolism, stress response, and virulence and/or pathogenesis. A number of family members have been demonstrated to be involved in pathogenesis, regulating the elaboration of virulence factors of microorganisms that infect plants and mammals (10). A well-characterized AraC family member that is involved in pathogenesis is ToxT, which has been shown to activate expression of the toxin coregulated pilus and cholera toxin in Vibrio cholerae (6). ToxT has further been shown to perform a dual regulatory task: inhibition of repression and direct activation (reviewed in reference 8). The predicted product of the perA gene from the MMH594 PAI is similar to the MsmR protein from Streptococcus pyogenes. MsmR has been shown to transactivate the expression of the major fibronectin-binding adhesion protein, as well as positively regulate the cytolysin-mediated translocation system genes (24).
The close proximity of the perA gene to a number of well-characterized virulence determinants on the E. faecalis pathogenicity island, as well as the fact that AraC/XylS members are known to regulate virulence factors in other pathogens, suggests a possible role in the regulation of these virulence determinants. as well as other uncharacterized PAI genes. Moreover, it has recently been demonstrated that an AraC-type ORF encoded on the putative E. faecium PAI regulates Esp and is involved in biofilm formation (R. Willems et al., unpublished data). In E. faecalis, the fsr regulatory locus has been implicated in regulation of biofilm formation through the control of gelatinase (15), and three ArgR family regulators were also identified as involved in biofilm formation (18). Further, the EbpR regulator, which shows similarities to a AtxA/MgaA family member, has been implicated in biofilm formation through the activation of genes encoding a piluslike structure (1). However, the involvement of AraC/XylS family members in biofilm formation has not been evaluated in E. faecalis.
In the present study, expression of the perA gene was evaluated in E. faecalis strain MMH594, the strain possessing the prototype PAI, as well as in the urinary tract isolate E99. In order to examine the potential role of the perA gene in biofilm formation and pathogenesis, the perA gene was insertionally inactivated in strain E99, and the resultant perA mutant strain was compared to the wild type in in vitro biofilm and macrophage survival assays and in a mouse peritonitis model.
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TABLE 1. Bacterial strains and plasmids used in this study
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TABLE 2. Primers used in this study
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Insertional inactivation of the perA gene in strain E99. In order to generate a insertional mutant in the perA gene, a 550-bp internal fragment of the perA gene was amplified using the primer pair perA-13F and perA-14R (Table 2) and E99 genomic DNA as a template. The resultant product was treated with PstI and EcoRI and ligated to the similarly restricted suicide vector p3ERM (2, 14). The resulting plasmid construct, p3ERMperA, was then introduced into electrocompetent E99 by electroporation as previously described (32). Erythromycin-resistant clones were selected, and insertion of the vector into the perA gene was verified by Southern hybridization analysis and PCR. Southern analysis demonstrated a single insertion in the perA locus, ruling out the possibility that the observed phenotypes were due to insertion in other locations. The perA insertion mutant strain was designated DBS01. To rule out a polar effect of insertion of the p3ERMperA plasmid into the perA gene, expression analysis of the gene located immediately 3' of perA on the PAI revealed no differences in expression between E99 and the perA mutant strain DBS01 using RNA derived from the logarithmic phase of growth (data not shown). The mutant DBS01 was complemented in trans using pGT101, a derivative of the shuttle vector pAT28 (40) possessing a full-length copy of the perA gene, including the putative E99 native promoter region. The plasmid pGT101 was constructed by PCR amplification of the perA gene using the primer pair perA-compF and perA-compR (Table 2), restriction of the amplicon with BamHI and EcoRI, and ligation of the product to similarly restricted pAT28.
Biofilm assay. In order to determine whether the PerA regulator influences biofilm formation, a crystal violet staining assay was used essentially as described by Tendolkar et al. (38). E. faecalis strains E99, DBS01, and DBS01(pGT101) were grown at 37°C for 16 h in TSB plus 0.75% glucose or in THB plus 1% glucose and the appropriate selective antibiotics. Following this growth period, bacterial cells were centrifuged at 6,000 x g for 10 min, and the cell pellet resuspended in 5 ml of fresh medium. The optical densities of the bacterial suspensions were measured by using a UV-1201 UV-VIS spectrophotometer (Shimadzu, Kyoto, Japan) and normalized to an optical density at 600 nm of 1.0. Bacterial cultures were then diluted 1:40 in fresh TSB plus 0.75% glucose or in THB plus 1% glucose and the appropriate antibiotics. From the diluted culture, 200 µl was dispensed into 12 wells in a single row of a sterile 96-well flat-bottom polystyrene microtiter plate (Corning, Inc., Corning, NY). After incubation at 37°C for 24 h, the medium was aspirated, and the wells were washed three times with sterile phosphate-buffered saline (PBS). The plates were inverted and allowed to dry for 1 h at room temperature. For biofilm quantification, wells were stained with 200 µl of 0.2% aqueous crystal violet solution for 15 min and washed thrice with sterile PBS to remove the excess crystal violet. Crystal violet bound to the biofilm was extracted with 200 µl of an 80:20 (vol/vol) mixture of ethyl alcohol and acetone, and the absorbance of the extracted crystal violet was measured at 595 nm with an ELX-800 (Bio-Tek Instruments, Inc., Winooski, VT) automatic microplate reader. All biofilm assays were performed in triplicate, with 12 replicates for each strain per assay.
Intraperitoneal mouse infection model. Bacteria were cultivated overnight at 37°C in THB containing 1% glucose supplemented with appropriate antibiotics. The bacteria were collected by centrifugation at 6,000 x g for 10 min, washed twice in PBS (pH 7.4), and resuspended in 5% hog gastric mucin (pH 7.0; Pfaltz and Bauer, Waterbury, CT) at a concentration of 1.0 x 109 CFU/ml. Six-week-old female BALB/c mice (Harlan Sprague-Dawley, Indianapolis, IN) were administered 200 µl of the suspension (2.0 x 108 CFU) via intraperitoneal injection. Control mice were also injected with 200 µl of 5% hog gastric mucin without bacteria to ensure both the sterility of the mucin and the absence of antibiotic-resistant bacteria in the tissues to be sampled. Control animals were treated in a manner identical to the experimental groups in all respects. Groups of 10 mice per strain were sacrificed at 24, 48, and 72 h by CO2 asphyxiation. From each animal, samples of blood were taken by cardiac puncture, and samples of the liver and spleen were taken by dissection. Liver and spleen samples from each time point were placed into preweighed 2-ml screwcap microcentrifuge tubes containing 0.5 ml of 1.0-mm zirconia/silica beads (BioSpec Products, Bartlesville, OK). Tubes were weighed to determine the size of the tissue sample, and 1 ml of PBS (pH 7.4) was then added. Tubes were shaken horizontally at 5,000 rpm for 1 min in a Mini-Beadbeater (BioSpec Products). Bacteria were enumerated via serial dilution and plating of the blood and tissue homogenates on BHI agar containing appropriate antibiotics. Bacterial concentrations were expressed as CFU/ml for blood and as CFU/g for the liver and spleen. The nonparametric Wilcoxon/Kruskal-Wallis test was used to determine significance levels.
Transmission electron microscopy. RAW 264.7 macrophages (American Type Culture Collection [ATCC], Manassas, VA) were cultivated in Dulbecco modified Eagle medium (DMEM; ATCC 30-2002) plus 10% fetal bovine serum (FBS; ATCC 30-2020) to confluence in T-25 flasks. Cells were harvested, and viability determined by trypan blue dye exclusion staining. Approximately 106 cells were seeded into each well of six-well plates, followed by incubation at 37°C under 5% CO2 for 24 h prior to infection. E. faecalis strains E99, DBS01, and DBS01(pGT101) were grown in THB containing 1% glucose and supplemented with the appropriate antibiotics for 16 h, centrifuged, and resuspended in PBS (pH 7.4). RAW 264.7 cells were infected at a multiplicity of infection (MOI) of 100 for each bacterial strain for 1 h at 37°C under 5% CO2, washed twice with PBS, and further incubated with DMEM plus 10% FBS containing 16 µg of vancomycin per ml and 150 µg of gentamicin per ml. At 0, 2, 24, 48, and 72 h postinfection, the cells were harvested; centrifuged at 1,000 x g for 5 min; and resuspended in 500 µl of a fixative solution consisting of 4% paraformaldehyde, 2% glutaraldehyde (Electron Microscopy Services, Hatfield, PA), and 0.1 M sodium cacodylate (Sigma, St. Louis, MO). Fixed cells were dehydrated and embedded in Epon/Araldite resin, cured, and sectioned. Sections (100 nm thick) were placed on glow-discharged 300 Cu Mesh grids and lead/uranyl acetate stained using Sato's lead. Cells were then imaged on a Hitachi H-7600 transmission electron microscope.
Macrophage survival assay. Survival of E. faecalis strains in macrophages was assessed essentially as described earlier (37). RAW 264.7 macrophages were seeded into six-well plates at approximately 106 cells per well and incubated at 37°C under 5% CO2 for 24 h prior to infection. E. faecalis strains E99, DBS01, and DBS01(pGT101) and E. coli XL1-Blue were grown in THB containing 1% glucose and supplemented with the appropriate antibiotics for 16 h, centrifuged, and resuspended in PBS (pH 7.4). Triplicate wells of RAW 264.7 cells were infected at an MOI of 100 for each bacterial strain for 1 h at 37°C under 5% CO2, washed twice with PBS, and further incubated with DMEM plus 10% FBS containing 16 µg of vancomycin per ml and 150 µg of gentamicin per ml for 2, 24, 48, and 72 h. Importantly, E. faecalis strains E99, DBS01, and DBS01(pGT101) demonstrate equivalent susceptibilities to the bactericidal activity of these two antibiotics. At each time point, the macrophages were washed twice with PBS (pH 7.4) and harvested in 1 ml of PBS (pH 7.4), the viability was assessed by trypan blue staining, and the macrophages were counted with a hemacytometer. Macrophages were then lysed by adding 100 µl of a saponin cell lysis solution (saponin [40 mg/ml], polypropylene glycol [P-2000; 8 ml/liter], sodium polyanetholsulfonate [9.6 mg/ml]) to release intracellular bacteria. Bacteria were quantified by serial dilution and plating. The number of viable bacteria at each time point was expressed as CFU per 105 macrophages. Experiments were performed three times, and the means and standard errors were determined for each time point. The statistical significance of the results was determined by performing pairwise comparisons at each time point using the Wilcoxon/Kruskal-Wallis test.
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1.5 kb 3' to the esp (for enterococcal surface protein) gene on the MMH594 PAI and was designated perA (for pathogenicity island-encoded regulator). The deduced PerA consists of 331 amino acids with a putative helix-turn-helix DNA-binding domain located within the C-terminal 100 amino acids. In order to determine perA gene expression in MMH594, RT-PCR was conducted using RNA isolated from bacteria grown to logarithmic and stationary phases in BHI broth. Interestingly, RT-PCR did not yield a detectable product from RNA derived from strain MMH594 grown in BHI to either stationary (Fig. 1) or logarithmic (data not shown) phase. Tendolkar et al. (39) have recently characterized a high-biofilm-forming clinical isolate of E. faecalis, designated E99 and identified a novel locus encoding putative surface proteins responsible for the high-biofilm-forming phenotype. This strain also possesses portions of the PAI, including the perA gene. It was therefore of interest to examine the expression of the perA gene in this high-biofilm-forming infection-derived isolate. RT-PCR analysis revealed expression of the perA gene in the stationary phase of growth in BHI (Fig. 1). The predicted PerA protein in E99 is identical to that of MMH594 with the exception of 71 additional N-terminal amino acids in the E99 polypeptide. Alignment of the C-terminal 100 amino acids of the E99 PerA with the consensus AraC helix-turn-helix motif (10, 20) revealed 33% identity and 38% similarity.
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FIG. 1. Expression of perA in MMH594 and E99 by RT-PCR. Primers perA-FF and perA-RR (Table 2), specific to perA, were used in all reactions. RT(–) controls indicate samples are free of contaminating genomic DNA. Lanes: 1, E99 DNA; 2, E99 RT(+); 3, MMH594 RT(+); 4, E99 RT(–); 5, MMH594 RT(–); 6, MMH594 DNA. Lane M is a 1-kb size marker from New England Biolabs.
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FIG. 2. Position of esp, IS1191, and perA in MMH594 (29) and E99. The sequence containing a potential consensus promoter is denoted by the dashed line, and the predicted extended perA sequence as part of the ORF is denoted by the checkered box.
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5-fold (38). However, we detected no difference in the biofilm density between strain E99 and DBS01 (P = 0.34) (data not shown), suggesting that the perA gene does not play a role under these conditions. We therefore evaluated additional laboratory media for possible medium-dependent effects. After growth of the three strains in THB plus 1% glucose, we observed a statistically significant increase in biofilm formation by the DBS01 strain relative to both E99 (P < 0.0001) and the mutant complemented strain DBS01(pGT101) (P < 0.0001) (Fig. 3). No significant difference was observed between E99 and DBS01(pGT101) (P = 0.23) (Fig. 3). No differences in in vitro growth rates were observed between the three strains in BHI, TSB plus 0.75% glucose, or THB plus 1% glucose (data not shown). These results show that inactivation of the perA gene in strain E99 results in approximately a 30% increase in biofilm formation after growth in THB plus 1% glucose, suggesting that the PerA regulator likely represses factors that contribute to this process in a medium-dependent fashion.
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FIG. 3. Biofilm density after growth in THB plus 1% glucose. Biofilm formation by E. faecalis strains E99, DBS01, and DBS01(pGT101) on polystyrene microtiter plates was assessed by crystal violet staining. Biofilm assays were performed in triplicate, with 12 replicates for each strain per assay. The error bars represent the means ± the standard errors. A Student t test was used to determine significance levels.
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FIG. 4. Bacterial load at 24 (A), 48 (B), and 72 (C) h in the liver, spleen, and blood for mice given E. faecalis strains via intraperitoneal injection. Error bars represent means ± the standard errors. A nonparametric Wilcoxon/Kruskal-Wallis test was used to determine significance levels.
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FIG. 5. Transmission electron microscopy of RAW 264.7 macrophages at 0 h (A, B, and C), 2 h (D, E, and F), 24 h (G, H, and I), 48 h (J, K, and L), and 72 h (M, N, and O) after infection with E. faecalis strains E99 (A, D, G, J, and M), DBS01 (B, E, H, K, and N), and DBS01(pGT101) (C, F, I, L, and O). Arrows indicate bacterial cells inside macrophages.
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FIG. 6. Intracellular survival of E. faecalis strains E99, DBS01, and DBS01(pGT101) in RAW 264.7 macrophages at 2, 24, 48, and 72 h postinfection. The number of viable bacteria at each time point is expressed as CFU per 105 macrophages. Experiments were performed three times, and the means and standard errors are reported for each time point. A nonparametric Wilcoxon/Kruskal-Wallis test was used to perform pairwise analyses at each time point.
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In strain MMH594, perA is located
1.5 kb 3' to the esp gene, with an IS1191 element situated between the two genes. Examination of the intergenic region 3' to the IS1191 element and 5' to the putative perA coding sequence did not reveal consensus bacterial promoter elements. RT-PCR confirmed that MMH594 did not express the perA regulator under the conditions examined. However, screening of a collection of 53 geographically diverse clinical and non-infection-derived isolates containing a broad array of insertions and deletions in the PAI revealed the presence of the putative perA gene in 51 of these isolates (S. McBride et al., unpublished data). These results suggest that insertion of the IS1911 has disrupted the promoter region of the perA gene in strain MMH594; however, the overall impact of the apparent silencing of perA expression in this strain is currently unknown. Expression of the perA gene was detected in strain E99, and the product was predicted to possess an extended amino acid sequence at the N terminus relative to that from MMH594, although the impact this has on regulatory function remains unclear. There are no identifiable conserved sequences located within the N-terminal region of PerA in MMH594 or E99, and there are no similarities in this region with other members of the AraC/XylS family of transcriptional regulators.
The ability to form biofilms is an important aspect of the E. faecalis infection process (3, 22, 25). Mohamed et al. (22) suggested that endocarditis isolates were more likely to form biofilms than were nonendocarditis isolates, and disruption of the ebp locus in strain OG1RF resulted in a decrease in the ability to form biofilms and concomitant attenuation in an endocarditis model (25). A number of E. faecalis regulators have been demonstrated to be involved in the formation of biofilms, including the fsr regulatory locus that controls the expression of gelatinase (GelE), a factor required for this process (15), as well as three different members of the ArgR family of transcriptional regulators (18). Given the proximity of the perA gene to esp, which has been shown to contribute to biofilm formation in a glucose-dependent manner, we postulated that PerA might be involved in regulating biofilm formation. Crystal violet staining of biofilms revealed that the PerA regulator influences biofilm formation in a growth medium-dependent manner, i.e., a role for PerA in biofilm formation was observed after growth in THB plus 1% glucose but not TSB plus 0.75% glucose. Given that Esp enhances biofilm formation in both types of media (data not shown), a likely explanation for these observations is that in THB plus 1% glucose factors other than Esp are being regulated by PerA and playing a role in biofilm formation. This idea is supported by preliminary observations which suggest that esp expression may actually be downregulated
2-fold in the perA mutant (data not shown). Although it remains unclear what factors in the growth medium are influencing PerA regulation of biofilm formation, it has previously been demonstrated that Rbf, a member of the AraC/XylS family of transcriptional regulators, regulates biofilm formation in S. aureus in a glucose- and NaCl-dependent manner and impacts biofilm formation at the multicellular aggregation stage (20). Experiments are currently under way to identify the additional factors that may be subject to PerA regulation.
Given the location of the perA gene on the E. faecalis PAI, it was of particular interest to explore the role of PerA in pathogenesis. In order to determine the effect of PerA, a murine model of intraperitoneal and systemic infection was used (7, 17). The results clearly demonstrate that PerA contributes significantly to the pathogenicity of E99 in this particular model of systemic E. faecalis infection and identify PerA as a new regulator and the only AraC/XylS-type transcriptional regulator in E. faecalis currently ascribed a role in pathogenesis. Based on these results, we postulated that the increased bacterial load of wild-type E99 in hepatic and splenic tissues might be due to the ability to survive the oxidative burst within phagocytes. AraC-type family regulators are known to play a role in the stress response (10). An AraC-type regulator in Salmonella enterica, designated RamA, confers resistance to oxidative killing in vitro but not in vivo (41). E. faecalis is well recognized for its inherent ability to survive intracellular killing by phagocytes, and this trait may provide a mechanism for E. faecalis to cause systemic disease. Gentry-Weeks et al. (11) reported that E. faecalis persists in murine peritoneal macrophages for 72 h. Gilmore et al. (13) have proposed that nosocomial enterococcal infection arises from colonization of new gastrointestinal tract niches by hospital isolates of enterococci after treatment with antibiotics with little or no anti-enterococcal activity. These strains expand and translocate across the gastrointestinal tract and are then trafficked to a regional lymph node by macrophages (46, 47). Resistance to killing would therefore provide a mechanism to persist at extraintestinal sites, and thus understanding the mediators of this phenotype is important to the development of new therapies.
Studies of the regulation of the response to oxidative stress in E. faecalis have revealed a number of different regulators, including HypR, a member of the LysR family (45); a PerR-like polypeptide (44); and a PrfA-like protein designated Ers (12, 27). Verneuil et al. (45) demonstrated that a hypR mutant strain was significantly more sensitive to a hydrogen peroxide challenge and phagocytic killing than the wild-type strain and was attenuated in a mouse peritonitis model (43). Recently, a thiol peroxidase designated Tpx was identified as a target for HypR regulation, and a tpx deletion mutant was found to be impaired in macrophage survival (19). Verneuil et al. (44) also characterized a regulator with similarities to the peroxide regulator PerR in Bacillus subtilis. Interestingly, although a perR mutant strain displayed increased resistance to hydrogen peroxide relative to a wild-type strain, it did not exhibit any difference from the wild type in the ability to survive in mouse peritoneal macrophages (44). The authors of that study also demonstrated that the PerR is important for virulence, apparently through a mechanism different from the response to oxidative stress (44). However, the PerR regulon in E. faecalis remains undefined.
Giard et al. (12) recently identified a transcriptional regulator of E. faecalis, designated Ers (for enterococcal regulator of survival). This regulator was classified as a member of the Crp/Fnr family and showed a high degree of similarity to a PrfA-like regulator implicated in virulence of Streptococcus pyogenes (12, 26). These authors further demonstrated a role of this regulator in macrophage survival and resistance to oxidative stress and subsequently identified several genes that represent regulatory targets, including genes encoding members of the arginine deiminase system, a gene encoding citrate lyase, and a gene, EF_1459, encoding a hypothetical protein (27). However, the function of these gene products in macrophage survival is unclear, since targeted mutations in these genes did not result in any difference in macrophage survival ability (27).
Muller et al. evaluated the involvement of 8 of the two-component regulatory systems in E. faecalis in mediating resistance to killing by macrophages (23). Mutations in the cognate regulator component of the two-component system Err04-Ehk04 resulted in significant attenuation in the ability to survive in macrophages. Mutations in the Err05 and the Err06 genes seemed to influence survival as well. However, these results are difficult to interpret given that these mutants seemed to be poorly phagocytosed relative to the wild-type JH2-2 strain, i.e., these mutants were detected at 1 to 2 orders of magnitude lower than the wild type at the beginning of the assay (23). In a similar study, Verneuil et al. (42) showed that a mutant strain lacking the manganese-containing superoxide dismutase (sodA) was more susceptible to killing by murine peritoneal macrophages. This indicates a mechanism by which E. faecalis can resist the respiratory burst within macrophages. Whether the ability of PerA to influence survival within macrophages is due to its effect on resistance to oxidative killing remains to be investigated.
The identities of the regulatory targets of PerA in E. faecalis strain E99 are currently unknown. Given the location of the perA gene on the E. faecalis PAI, we have hypothesized that PAI genes, such as those encoding the enterococcal cytolysin, Esp, and aggregation substance, might represent PerA regulatory targets. Gentry-Weeks et al. (11) were not able to demonstrate a role for the cytolysin in macrophage survival; however, it was unclear whether this toxin was actually expressed intracellularly. Although the role of the esp gene has not been directly assessed in macrophage survival, aggregation substance, a surface-associated protein that promotes conjugative plasmid transfer by mediating cell to cell contact, has been shown to play a role in resisting macrophage killing (37). The authors of that study showed that strains expressing aggregation substance were more adherent and internalized to a greater degree than aggregation substance negative strains but were more resistant to phagocytic killing apparently through inhibition of the respiratory burst (37).
In summary, we have identified a gene on the E. faecalis PAI that encodes a putative transcriptional regulator involved in regulation of biofilm formation, pathogenesis, and intracellular macrophage survival. Experiments are currently under way to further elucidate the regulatory role of PerA in these processes in E. faecalis.
We thank Nikki Craig, Miriam Kebaya, Toby Allen, Xingmin Wang, Tamara Hunt, and Roman Wolf for technical support; Joe Wilkerson at the Oklahoma Medical Research Foundation for performing the transmission electron microscopy; and Mark Huycke for helpful discussions.
Published ahead of print on 29 September 2008. ![]()
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