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Infection and Immunity, February 2006, p. 940-946, Vol. 74, No. 2
0019-9567/06/$08.00+0 doi:10.1128/IAI.74.2.940-946.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Mirjam Peter,2 and
Klaus Heeg2
Institute of Medical Microbiology, Philipps-University Marburg, Marburg, Germany,1 Department of Hygiene and Medical Microbiology, University Hospital Heidelberg, Heidelberg, Germany2
Received 2 August 2005/ Returned for modification 4 September 2005/ Accepted 30 October 2005
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It was noted early that stimulation by bacterial DNA could be mimicked by the use of [CG]-containing synthetic oligodesoxynucleotides (CpG-ODNs) (11). Since CpG-ODNs turned out to possess a considerable potential for immune modulation and since these compounds were easy to synthesize, subsequent work in the TLR-9 field has mainly focused on the use synthetic ODNs. It is intriguing that, despite the fact that basic principles in bacterial DNA/TLR-9 recognition have been known for years, information concerning the meaning of TLR-9 for infections or for the recognition of bacteria is still extremely limited.
Differences in the C/G composition (implying differences in [CG] content) are typical for different genera of bacteria. Since TLR-9 recognizes [CG]-containing DNA motifs, it can be speculated that DNA from different bacteria should vary in the TLR-9 activating capacity. In one study, DNA from four bacterial species had been analyzed, with Escherichia coli showing the highest activation and [CG] content (16). However, only a limited number of bacterial species have been tested, and the readout system was prone to activation by contaminants. Other studies analyzing side effects in plasmid vaccination showed that immunostimulation by plasmid DNA vectors correlated with [CG] content and that methylation (9) or elimination (27) of these motifs decreased immunostimulation. The data can be taken to hypothesize that the frequency of [CG] might be the basis for differences in immunostimulation by bacterial DNA. With the identification of more and more whole genomes of bacteria, it has become feasible to calculate for the real [CG] dinucleotide content in bacterial DNA.
Another question regarding the stimulation of TLR-9 has been whether sufficient concentrations of bacterial DNA can be reached to activate the receptor during infections. It is known that TLR-9 becomes activated within a lysosomal compartment and that DNA has to be taken up previously (1, 5, 13). As has been suggested for CpG-ODN/TLR-9 and RNA/TLR-7/-8, increasing the delivery efficiency seems to increase immunostimulation (6, 26). Whether this holds true for bacterial DNA from different species is not known.
In the present study we sought to analyze the effects of DNA preparations of 15 different bacteria in a TLR-9 specific reporter system.
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Cells and culture conditions. RAW 264.7 cells, a murine macrophage cell line, were kindly provided by R. Schumann, Berlin, Germany. HEK293 cells were obtained from S. Bauer, Munich, Germany. Cells were cultured in Clicks/RPMI 1640 supplemented with either 5% fetal calf serum (FCS; for RAW264.7) or 10% FCS (HEK293 cells), 50 µM ß-mercaptoethanol, and antibiotics (penicillin G and streptomycin). HEK-TLR9 cells were obtained by transfecting HEK293 cells with a human TLR-9-green fluorescent protein (GFP) expression plasmid (obtained from T. Espevik, Trondheim, Norway), and selection for stable expression in 0.8 mg of G418/ml. Cells were cloned and analyzed for CpG-DNA responsiveness.
Bacteria. Bacteria were obtained from an in-house library. The following strains were used Campylobacter jejuni (patient isolate), Corynebacterium efficiens (DSM 44549), Enterococcus faecalis (ATCC 29212), Escherichia coli (ATCC 25922), Klebsiella pneumoniae (ATCC 700603), Legionella pneumophila (wild-type corby strain, K Heuner, Wuerzburg, Germany), Mycobacterium tuberculosis (ATCC 27294), Neisseria meningitidis (patient isolate), Propionibacterium acnes (ATCC 6919), Pseudomonas aeruginosa (ATCC 27853), Salmonella enterica serovar Typhi (MCCM 01631), Staphylococcus aureus (ATCC 29213), Staphylococcus epidermidis (ATCC 12228), Streptococcus pneumoniae (patient isolate), and Yersinia enterocolitica (MCCM 01839).
DNA preparation. Bacteria were grown in 30 ml of Luria-Bertani medium, in brain heart infusion, or on solid Schaedler plates and subsequently pelleted. Bacterial DNA was prepared suspending the bacteria in 20 mM Tris-HCl-0.2 mM EDTA (pH 8.0). Lysozyme (20 mg/ml) was added for 30 min at 37°C. Next, the samples were incubated in 100 mM NaCl-10 mM Tris-HCl-25 mM EDTA (pH 8.0) with proteinase K (0.2 mg/ml) and sodium dodecyl sulfate (0.5%) at 50°C overnight. DNA was purified from the lysate by repeated extraction with phenol-chloroform-isoamyl alcohol, precipitated with sodium acetate, and ethanol and then dissolved and stored at 20°C in aliquots. DNA content and purity were measured spectroscopically.
Western blotting. A total of 5 x 106 cells were lysed for 30 min on ice in 250 µl of lysis buffer (50 mM Tris-HCl [pH 7.4]; 1% Igepal; 0.25% sodium deoxycholate; 150 mM NaCl; 1 mM EDTA; 1 mM phenylmethylsulfonyl fluoride; aprotinin, leupeptin, and pepstatin [1 µg/ml each]; 1 mM Na3VO4; 1 mM NaF). Lysates were cleared by centrifugation at 4°C for 10 min at 11,000 x g. Equal amounts of lysates were fractionated by sodium dodecyl sulfate-10% polyacrylamide gel electrophoresis and electrotransferred to polyvinylidene difluoride membranes. Membranes were stained with anti-GFP antibody (Santa Cruz Biotechnology) and visualized by enhanced chemiluminescence system (Amersham, Freiburg, Germany).
Flow cytometry. TLR-9-GFP-transfected cells were analyzed for GFP expression on a PAS flow cytometer (Partec, Muenster, Germany).
Cell stimulation and cytokine measurement. A total of 2 x 105 HEK-TLR9 or 1.5 x 105 RAW264.7 cells were stimulated in 96-well plates in duplicates overnight. Cell-free supernatants were analyzed for cytokine secretion by enzyme-linked immunosorbent assay (ELISA; OptEIA; BD Pharmingen, Heidelberg, Germany).
Quantitative PCR. A total of 5 x 105 HEK-TLR9 cells were incubated with 10 µg of bacterial DNA/ml for 4 h. Cells were washed intensely four times and genomic DNA (host and bacteria) was prepared with Qiamp DNA kit (QIAGEN, Hilden, Germany). Quantitative PCR for GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and eubacterial 16S rRNA was performed on three dilutions of the DNA samples as described previously (17). 16S rRNA amplicons were normalized to GAPDH.
Bioinformatics. Genome data were analyzed with a software tool (GScan) developed by T. Mallée (Marburg, Germany) for this purpose. Sequence data were examined for the frequency of various nucleotide motifs by a string search.
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FIG. 1. Characterization of the HEK-TLR9 cell line. (a) HEK293 cells stably transfected with a human TLR9-GFP expression plasmid were analyzed for GFP expression by flow cytometry (filled curve, wild type; solid line, HEK-TLR9 cells) and by Western blotting with anti-GFP (inset). (b) HEK-TLR9 cells were stimulated with 1 µM CpG-ODN 2006, the control ODN 2006GC, or with 100 ng of LPS/ml overnight, and supernatants were examined for IL-8 secretion by ELISA (means of duplicates plus the standard deviations [SD], one of three experiments).
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FIG. 2. Bacterial DNA stimulates TLR-9. (a) HEK-TLR9 cells were activated with different concentrations of bacterial DNA preparations from E. coli or E. faecalis. Normalized IL-8 secretion (mean of duplicates) of one of two experiments is shown. (b) HEK-TLR9 cells were stimulated with CpG-ODN 2006, and 100 ng of LPS/ml was added as indicated. (c) HEK-TLR9 cells were incubated with DNA from E. faecalis, and 100 ng of LPS/ml was added as indicated. IL-8 secretion was determined by ELISA (means of triplicates plus the SD, one of two experiments each).
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FIG. 3. Bacterial DNA activates TLR-9 depending on the individual [CG] dinucleotide content. (a) Five independent bacterial DNA preparations from each indicated species (100 µg/ml) were tested for their activity on HEK-TLR9 cells. IL-8 secretion normalized to 3 µM CpG-ODN 2006 is shown as the mean of n = 5 experiments plus the standard error of the mean. (b) Mean values (n = 5) of normalized IL-8 secretion of the different bacteria are plotted against the individual frequency of the dinucleotide [CG] (fCG).
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1.0). However, there was an overrepresentation (pCG > 1.23) of [CG] in Salmonella enterica serovar Typhi and an underrepresentation (pCG < 0.78) in Streptococcus pneumoniae and Campylobacter jejuni. Also, the murine genome showed a severe underrepresentation of [CG]. Differences in fCG in general went along with differences in the frequency of [TCG], as well as the optimal murine CpG motive [Pu-Pu-C-G-Py-Py]. |
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TABLE 1. Microbial genome sequence analysis
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Intracellular delivery of bacterial DNA increases stimulation of TLR-9. CpG-DNA has to be taken up in cells in order to stimulate intracellularly expressed TLR-9. We tested whether delivery of bacterial DNA by the transfection reagent DOTAP affects stimulation of TLR-9. Using eubacterial 16S rRNA PCR to measure uptake of bacterial DNA, we observed first that DNA samples from E. coli and E. faecalis indeed were taken up into HEK-TLR9 cells (Fig. 4a). Uptake of E. faecalis DNA seemed to be slightly more efficient than for E. coli, but differences were not significant. Moreover, analyzing uptake of DNA from all bacteria tested confirmed that only minor differences occurred which could not explain the differences in immunostimulation (data not shown). Using DOTAP packaged DNA there was a great increase in the uptake of bacterial DNA (20-100-fold) (Fig. 4a). In parallel stimulation of TLR-9 by low concentrations of DNA (10 µg/ml) was examined. Without DOTAP IL-8 secretion was only low, with E. coli being more active than E. faecalis (Fig. 4b). Upon delivery with DOTAP both DNA preparations increased in their capacity to activate TLR-9 (2- and 2.5-fold increase for E. faecalis and E. coli, respectively). Still, DNA from E. faecalis despite of similar uptake was less active than DNA from E. coli, indicating that differences in immunostimulation do not depend on different cellular delivery.
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FIG. 4. Increased intracellular delivery of bDNA improves stimulation of TLR-9. (a) HEK-TLR9 cells were stimulated with 10 µg of bacterial DNA/ml, which was delivered by the transfection reagent DOTAP as indicated. Cells were analyzed for uptake of bacterial DNA by means of quantitative eubacterial PCR. 16S rRNA gene amplicons were normalized to GAPDH (mean values plus the SD; controls, n = 6 experiments; DOTAP, n = 4). (b) Additionally, IL-8 was measured in the supernatant (mean values plus the SD, n = 3; medium, 15.1 ± 0.9 pg/ml). (c) RAW264.7 macrophages were stimulated with bacterial DNA from E. faecalis (triangles) or S. aureus (circles) either without (filled symbols) or with (open symbols) DOTAP. Tumor necrosis factor alpha (TNF- ) was measured in overnight supernatants by ELISA (means of duplicates of one of two experiments).
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/ml; plus DOTAP, 15.2 ± 2.2 ng/ml, n = 3). |
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The present study is based on the use of a TLR-9/DNA specific reporter system that exclusively measured activation by the DNA fraction. This is important since we and others have observed that rather high concentrations of DNA are necessary to stimulate TLR-9 (18, 19), and thus even minute amounts of contaminating TLR ligands might lead to wrong results if cells with a more complete set of TLRs are used. Therefore, we have adopted the well-known HEK-TLR complementation system for our purposes, as already reported by others for CpG-ODNs (2, 22). This system was exclusively responsive to CpG- but not GpC-ODNs. Among possible contaminants LPS is of special concern due to its high immunostimulatory capacity, and substimulatory doses have been shown to synergize powerfully with DNA (4). In our system neither LPS alone nor LPS in the coincubation setting with CpG-ODN or bacterial DNA influenced the experimental readout. Additionally, we analyzed the DNA preparations in HEK293 cells transfected with TLR-2, TLR-4, or NOD2 (data not shown). Samples from gram-negative bacteria showed residual TLR-4 activation indicative of minor LPS contamination, but all samples were inactive for TLR-2 or NOD2 stimulation. Of note, the HEK-TLR9 system did only work with stable transfectants but not with transient transfection. This might be due to an intrinsic stimulation during the transfection process since plasmid DNA has been reported to activate TLR-9 (20).
Upon analyzing TLR-9 activation by DNA from different species, we observed a wide range of stimulatory activity. Despite some variance the results could consistently be reproduced. In line with our results, a study from Neujahr et al. (using a different system and only four bacteria) also observed an improved activity of E. coli DNA over S. aureus DNA (16). In our study we for the first time were able not only to analyze TLR-9 activation but also to correlate this with genome sequence data. We analyzed genome data for frequencies of [CG] dinucleotides and were able to observe a positive correlation with immunostimulatory properties. High frequencies of [CG] could be observed for P. aeruginosa and M. tuberculosis and indeed the DNA fraction of M. tuberculosis had once been the starting point for identification of DNA immunostimulation (23). Other organisms, including E. coli and serovar Typhi, whose DNA preparations have commonly been used had intermediate [CG] frequencies. The results support the view of a [CG] content-dependent immunostimulation in bacterial DNA. In line with our results, others have shown that [CG] frequency in plasmids is correlated with immunostimulation in DNA vaccination (9, 27). It has also been suggested that some DNA sequences derived from adenoviruses (10) or composed of poly[G] (21) might inhibit TLR-9. However, we observed a clear positive correlation and thus were not able to confirm inhibitory sequences within the analyzed DNA samples.
Based upon these results the stimulatory potential of DNA is in the range of 1 to 100 µg/ml. One can calculate that this translates to rather high numbers of bacteria. Thus, stimulation of TLR-9 in real infections might be difficult to be achieved, yet synergism with other TLRs has been reported (3, 4, 28). Moreover, recently it was reported that increased delivery of RNA or CpG-ODNs with transfection reagents was able to enhance immunostimulation by TLR-7 and -9, respectively (6, 26). In line with this, we also observed that DOTAP delivered bacterial DNA efficiently into the cell, thereby increasing the local concentration. In parallel, this lowered the threshold for immunoactivation of TLR-9 by a factor of 10 to 100. The biological equivalent could be that TLR-9 activation by DNA is especially active if bacteria are enriched intracellularly. Indeed, TLR-9, but also TLR-7 and -8, is expressed intracellularly but not at the surface (1) and, accordingly, this whole group of nucleic acid-detecting receptors might serve a special function for only subgroups of microbes. Thus far, TLR-9-deficient mice have only been reported to be sensitive to herpes simplex virus and cytomegalovirus infection but not to bacteria (12, 14). Perhaps TLR-9-mediated activation through bacterial DNA is important only for few bacterial species. Thus, Propionibacterium acnes, which here showed rather high DNA-dependent immunostimulative activity, sensitizes mice for LPS by increasing gamma interferon, and this was dependent on TLR-9 (8).
Taken together, these findings show that activation of TLR-9 by bacterial DNA differs depending upon the bacterial species from which the DNA is prepared, and this correlates with the genomic frequencies of [CG] dinucleotides. Moreover, intracellular delivery of bacterial DNA increases the immunostimulatory potential.
We thank Christine Barett, Adelina Dillmann, and Stefanie Penati for excellent technical support.
Present address: Institute for Medical Parasitology, University Hospital Bonn, Bonn, Germany. ![]()
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B. Int. Immunol. 13:1391-1404.
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