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Infection and Immunity, October 2003, p. 5640-5649, Vol. 71, No. 10
0019-9567/03/$08.00+0 DOI: 10.1128/IAI.71.10.5640-5649.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19014 and,1 Department of Periodontics, Endodontics and Dental Hygiene, School of Dentistry, University of Louisville, Louisville, Kentucky 402922
Received 11 February 2003/ Returned for modification 22 April 2003/ Accepted 14 July 2003
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The leukotoxin is expressed from an operon consisting of at least four genes, designated ltxC, ltxA, ltxB, and ltxD, of which the ltxA gene encodes the structural toxin (28, 30). The three remaining genes are required for the activation and secretion of the leukotoxin. The ltxC gene is analogous to hlyC of the Escherichia coli hemolysin operon, which is involved in the acylation of the hemolysin protein (19). Although it has not yet been demonstrated in A. actinomycetemcomitans, it is likely that ltxC carries out a similar function. The ltxB and ltxD genes function in the signal peptide-independent secretion of the leukotoxin (29) and are homologous to hylBD of the E. coli hemolysin operon. In addition, an open reading frame (orfA) that encodes a putative polypeptide of unknown function exists upstream from ltxCABD and is cotranscribed with the ltx operon. Leukotoxin expression varies greatly among A. actinomycetemcomitans strains, but most strains express relatively low levels of toxin. However, several hyperleukotoxic strains have been identified (4, 15, 25) and recent studies suggest that these organisms are associated with human periodontal diseases (5, 10, 12, 14). Hyperexpression of leukotoxin in A. actinomycetemcomitans correlates with the presence of specific genetic rearrangements, both insertions and deletions, in the region immediately upstream of the ltx operon (4, 15). For example, in A. actinomycetemcomitans JP2, a deletion of 530 bp encompassing parts of orfA and the orfA-ltxC intergenic region results in a 10-fold increase in toxin expression (4). He et al. also showed that integration of IS1301 upstream from orfA in A. actinomycetemcomitans IS1 increases toxin expression by eightfold (15). A spontaneous revertant of IS1 which lost IS1301 exhibited significantly reduced leukotoxic activity (15).
The mechanisms by which genetic rearrangements in the ltx operon influence toxin expression are not understood, in part because relatively little is known about the regulatory mechanisms that govern leukotoxin expression. In this report, we show that the acquisition of IS1301 results in increased transcription of the ltx operon but that IS1301 does not possess an outwardly directed promoter that transcribes ltx sequences. In the ltx promoter, we identified a positive cis-acting sequence resembling an UP element downstream from the site of IS1301 insertion and a negative cis-acting regulator that resides upstream from IS1301. Our results suggest that IS1301 may disrupt normal regulation of the ltx operon and increase leukotoxin expression by displacing a negative cis-acting sequence 900 bp upstream from the basal ltx promoter elements.
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Construction of ltx promoter::lacZ reporter plasmids.
Reporter plasmids containing the glyA-ltxC intergenic region from A. actinomycetemcomitans strains 652 (652lacZ) and IS1 (ISlacZ) were constructed by amplifying the appropriate promoter fragment by PCR by using genomic DNA as a template. The promoter fragment from strain 652 was amplified by using primers 1 and 2 (Table 1); the promoter from strain IS1 was generated by using primers 3 and 2. Amplification reactions were carried out by using the following conditions: 95°C for 1 min, 55°C for 2 min, and 72°C for 3 min for 30 cycles. The PCR products were purified by using the QIA-quick PCR purification kit (Qiagen) according to the instructions from the manufacturer and cloned into pGEM-TEasy (Pharmacia). Plasmids were used to transform competent E. coli DH5
, and recombinants were selected on LB agar containing 50 µg of ampicillin per ml. Plasmid was isolated from recombinant organisms and confirmed by restriction digestion. Promoter fragments were subsequently released from pGEM-TEasy by digestion with KpnI and BamHI and ligated into pYGKlacZ that had been cleaved with the same enzymes. Plasmid pYGK is an E. coli-A. actinomycetemcomitans shuttle vector that is maintained at a copy number of approximately three to four copies per cell (3). Transformation of E. coli DH5
and confirmation of the desired plasmids were as described above except that recombinants were selected on LB agar containing 25 µg of kanamycin per ml. Purified plasmid obtained from recombinant E. coli cultures was subsequently introduced into A. actinomycetemcomitans 652 by electroporation according to the method of Sreenivasan et al. (51).
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TABLE 1. Oligonucleotide primers
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Construct IRL lacks the upstream portion of the AT-rich IR and was synthesized from two PCR products by using a strategy similar to that described above for clone IR20. The upstream promoter fragment was synthesized by using primers 1 and 6. The downstream fragment was identical to the fragment used as described above for the construction of IR20. Fragments were digested with the appropriate restriction enzymes, sequentially ligated into pUC19, and transferred into pYGKlacZ as described above.
Promoter fragments for the deletion constructs 191lacZ (primers 2 and 7), 197lacZ (primers 2 and 8), and 229lacZ (primers 2 and 9) were amplified by PCR from A. actinomycetemcomitans 652 genomic DNA by using the primer pairs indicated. Fragments were purified, cleaved with KpnI and BamHI, and ligated into pYGKlacZ as already described. All ltx promoter constructs were confirmed by nucleotide sequencing.
Determination of ß-galactosidase activity. Recombinant A. actinomycetemcomitans strains containing the lacZ reporter constructs were grown to mid-exponential phase and centrifuged to pellet bacterial cells. The cell pellets were washed and suspended in 0.1 M sodium phosphate, pH 7.5, at an optical density (OD) of 0.5 at 600 nm. ß-galactosidase activity was determined by using o-nitrophenyl-ß-galactoside (ONPG; Sigma Chemical Co.) as follows: 5 µl of cell suspension, 10 µl of 0.01% sodium dodecyl sulfate, and 25 µl of chloroform were added to 227 µl of 0.1 M sodium phosphate, pH 7.5. After incubation at 25°C for 10 min, 3 µl of Mg buffer (0.1 M MgCl2, 4.5 M ß-mercaptoethanol) and 66 µl of ONPG (4 mg per ml in 0.1 M sodium phosphate, pH 7.5) were added. Samples were incubated for 10 min at 37°C. Reactions were terminated by the addition of 0.5 ml of 1 M Na2CO3, and the relative levels of ß-galactosidase activity were determined by measuring the OD at 420 nm. All reactions were run in triplicate. Units of ß-galactosidase activity were calculated according to the method of Miller (37).
Preparation of bacterial cell extracts. For protein extraction, 5 ml of B-PER bacterial protein extraction reagent (Pierce) supplemented with a protease inhibitor cocktail (Sigma Chemical Co.) was added to frozen bacterial pellets. The cell pellets were thawed on ice and resuspended by pipetting until the suspension was homogeneous. The suspension was gently mixed at room temperature for 10 min, and lysates were centrifuged at 27,000 x g for 15 min at 4°C to remove cellular debris and insoluble proteins. Cleared extracts were dialyzed overnight at 4°C against a solution containing 20 mM HEPES (pH 7.9), 2 mM MgCl2, 1 mM dithiothreitol (DTT), 1 mM EDTA, and 20% glycerol supplemented with 1 ml of protease inhibitor cocktail per liter, followed by dialysis for 8 h against a solution containing 20 mM HEPES (pH 7.9), 40 mM KCl, 1 mM DTT, 1 mM EDTA, 0.2 mM MgCl2, and 20% glycerol. Cell extracts were stored at -70°C.
Phosphocellulose chromatography. Cellulose phosphate ion exchanger P11 (Whatman) was prepared according to the manufacturer's instructions, and chromatography was carried out essentially as described by Samuels et al. (44). Prior to loading of the crude cell extract, the column was washed with three column volumes of a solution containing 20 mM HEPES (pH 7.9), 1 mM DTT, 1 mM EDTA, 0.1 M KCl, 0.2 mg of bovine serum albumin/ml, and 20% glycerol and subsequently with three column volumes of buffer A (20 mM HEPES [pH 7.9], 1 mM DTT, 1 mM EDTA, 40 mM KCl, 20% glycerol). Cell extracts were loaded onto the column, and nonspecifically bound material was removed by washing three times with buffer A. Bound protein was eluted with 1 M KCl. Fractions containing eluted protein were identified by ODs at 280 nm, pooled, and dialyzed against a solution containing 20 mM HEPES (pH 7.9), 1 mM DTT, 1 mM EDTA, 0.1 M KCl, and 20% glycerol. Phosphocellulose-fractionated extracts were stored at -70°C.
Analysis of protein interaction with the ltx promoter. Prior to use of protein extracts in gel shift assays, the suspensions were treated to remove biotin and/or biotin-containing proteins by incubation with magnetic beads derivatized with streptavidin (streptavidin MagneSphere paramagnetic particles; Promega). The streptavidin beads were washed three times before use with a solution containing 0.1 M NaCl, 10 mM HEPES (pH 7.9), and 5% glycerol. Bacterial cell extracts (100 µl) were incubated with the streptavidin beads (25 µl) for 15 min at 25°C, and subsequently, the beads were removed by using a magnetic separator. Routinely, crude bacterial cell extracts were extracted three times with streptavidin beads; the phosphocellulose-fractionated extracts were treated with a single application of streptavidin beads.
Promoter fragments B101, B101IR, B180, and B154 used in the mobility shift assays were amplified by PCR by using genomic DNA from A. actinomycetemcomitans 652 as the template. Primers used to produce the promoter fragments were as follows (Table 1): B101, primers 10 and 11; B101IR, primers 10 and 12; B180, primers 13 and 15; and B154, primers 13 and 14. To synthesize biotin-labeled probes, the upstream primer used in each reaction was modified with biotin at its 5' end. These primers were obtained from BioSynthesis, Inc. (Lewisville, Tex.). Promoter fragments B101IRL and B101IR20 were amplified by PCR with the primers used to produce B101IR. The templates for these reactions were plasmids pIRL and pIR20, respectively. Therefore, probes B101IRL and B101IR20 contain the modifications of the AT-rich IR sequence described above.
Analysis of protein-promoter interactions. Routinely, gel mobility shift reactions were carried out in a reaction volume of 10 µl containing 2 ng of biotinylated probe, 0 to 10 ng of unlabeled probe as a competitive inhibitor, 1 µg of poly(dI-dC), 2.5 µl of protein extract, 15 mM HEPES (pH 7.9), 24 mM KCl, 100 mM NaCl, 1 mM MgCl2, 1 mM DTT, 0.25 mM EDTA, and 5% glycerol. Mixtures for reactions that were carried out with unfractionated protein extracts contained 7.5 µg of protein and 1 µg of poly(dI-dC). Mixtures for reactions using phosphocellulose-fractionated protein extracts contained 0.3 µg of protein and 10 ng of poly(dI-dC). In all reactions, the biotinylated promoter probes were incubated with the protein extract at room temperature for 30 to 60 min. Reaction mixtures were loaded onto a 5% polyacrylamide gel and electrophoresed at 100 V in 1x Tris-borate-EDTA. The labeled probes and probe-protein complexes were subsequently transferred onto a HyBond N+ nylon membrane (Amersham Pharmacia Biotech) by using a semidry blotter (Bio-Rad, Inc.) at 12 to 15 V for 30 min. After the transfer was completed, the DNA was cross-linked to the membrane by exposure to UV light (1,200 µJ for 30 s) by using a UV Stratalinker 1800 (Stratagene). Detection of the labeled probes was accomplished by using a streptavidin-horseradish peroxidase conjugate and the BM chemiluminescence blotting substrate kit (Roche Diagnostics, Inc.) according to the manufacturer's protocol. Reaction products were visualized by exposure to Kodak X-Omat-AR X-ray film for 5 to 30 min.
To quantitate the formation of the probe-protein complex, digital images of each exposed film were analyzed by using Corel Photopaint. We first determined the background for each lane by dividing the total number of pixels (PTOT) that were present in a defined area of each lane (midway between the bands representing the protein-probe complex and the labeled probe itself) by the average grayscale level (IAVE) for these pixels. Grayscale level was expressed on a scale of 1 to 255 where black was 1 and white was 255. The resulting background level for each lane was then subtracted from the result of a similar analysis of the region encompassing the protein-probe complex band. Percent inhibition of complex formation by unlabeled probe at a given concentration, x, was calculated by using the following equation:
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Site-specific mutagenesis of the ltx promoter. Site-specific mutagenesis was carried out by using the Quikchange site-directed mutagenesis kit (Stratagene) according to the manufacturer's protocols. The plasmid template for mutagenesis reactions was pISlacZ. Reactions utilized oligonucleotide primers 23 and 24. Recombinant clones containing the mutations were confirmed by nucleotide sequencing. Confirmed clones were introduced into A. actinomycetemcomitans 652 and analyzed for lacZ expression as described above.
RT-PCR and real-time PCR with A. actinomycetemcomitans RNA. Real-time PCRs were performed by using Ready-To-Go reverse transcriptase PCR (RT-PCR) beads (Amersham Biosciences). A reaction volume of 50 µl was used to perform two reactions with 25 µl each. The RT step was carried out according to the manufacturer's instructions. Each reaction mixture contained 7.5 pmol of the appropriate antisense primer and 50 ng of total bacterial RNA. After completion of the cDNA synthesis, 7.5 pmol of the appropriate sense primer and 0.5x SYBR-Green dye (Roche Applied Science) were added. Amplification was carried out by using the Smart Cycler system (Cepheid). The amplification conditions for the real-time PCR were as follows: denaturation at 95°C for 270 s for a single cycle, followed by 45 cycles of denaturation at 95°C for 30 s, annealing at 56 or 58°C for 30 s, and elongation at 72°C for 60 s. The threshold cycle for each real-time PCR was determined from a second derivative plot of total fluorescence as a function of cycle number by using the software package supplied with the Smart Cycler system. The primers used for real-time PCRs were as follows: primer 16 (Table 1) anneals 15 nucleotides downstream from the transcriptional start site of the orfA promoter (Porf), and primers 18 and 19 anneal 95 and 42 nucleotides upstream from the Porf transcriptional start site, respectively. Each of these primers was used in conjunction with reverse primer 17, which anneals in the orfA open reading frame, or with reverse primer 20, which anneals to the 3' end of orfA. The annealing temperature for these reactions was 56°C. Control primers 21 and 22 anneal to the cytolethal distending toxin gene B (cdtB) of A. actinomycetemcomitans. The annealing temperature in these reactions was 58°C. All reactions were carried out at least two times with consistent results.
RT-PCRs were carried out by using Ready-To-Go RT-PCR beads (Amersham Biosciences) according to the manufacturer's instructions. Each reaction mixture contained 100 ng of total RNA and 15 pmol of the appropriate primers. cDNA synthesis was carried out at 42°C for 30 min, followed by a single cycle at 95°C for 5 min. Amplification conditions were as follows: 30 cycles of denaturation at 94°C for 60 s, annealing at 55°C for 60 s, and elongation at 72°C for 90 s. A. actinomycetemcomitans total RNA was isolated from mid-exponential-phase aerobic cultures by using TRIzol reagent (Invitrogen Life Technologies) according to the manufacturer's instructions. Contaminating genomic DNA was removed from the RNA preparations by digestion with RQ RNase-free DNase I (Promega).
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FIG. 1. IS1301 increases transcription of the ltx operon. (A) Schematic representation of the A. actinomycetemcomitans 652 and A. actinomycetemcomitans IS1 leukotoxin operons and upstream sequences. ltxA encodes the toxin polypeptide, and ltxC, ltxB, and ltxD encode toxin-activating and secretion proteins. orfA represents an open reading frame encoding a hypothetical protein of unknown function that is cotranscribed with ltxCABD. The upstream gene, glyA, encodes serine hydroxymethyltransferase and is not a part of the leukotoxin transcriptional unit. The locations of an AT-rich imperfect IR and -10 and -35 promoter elements of the orfA promoter (Porf) are shown. In A. actinomycetemcomitans IS1, a copy of IS1301 is integrated into the IR sequence. IS1301 carries a single gene, trnA, encoding a transposase (15). The arrows represent the annealing sites for oligonucleotide primers 16 to 20 used for RT-PCR and real-time PCRs. (B) Transcriptional activity of ltx promoter::lacZ reporter constructs. The glyA-ltxC intergenic regions of A. actinomycetemcomitans 652 and A. actinomycetemcomitans IS1 were fused to lacZ to generate constructs 652lacZ and ISlacZ, respectively. With the exception of the IS1301 sequence, the nucleotide sequences of the IS1 and 652 promoter fragments are >99% identical. For each construct, ß-galactosidase activity is shown on the right and was measured from cell extracts obtained from the recombinant strains by using ONPG as the substrate. (C) Real-time PCR results obtained by using total RNA from A. actinomycetemcomitans strains 652 and IS1. Reactions were carried out as described in Materials and Methods by using the primer pairs indicated. The cytolethal distending toxin B gene (cdtB) is transcribed independently of the ltx operon and was used in a control reaction in these experiments.
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FIG. 2. IS1301 does not possess an outwardly directed promoter. (A) The nucleotide sequence from the stop codon of trnA to the transcriptional initiation site of Porf is shown. The bold italic sequence is the terminal repeat of IS1301. The terminal repeat contains a putative -35 element (TTGTAC; underlined), indicated by the larger font, that is 18 nucleotides upstream from a potential -10 sequence (AATAAT; underlined). The -35 and -10 promoter elements of Porf are also labeled and underlined. The nucleotides that were substituted by site-specific mutagenesis are shown above the sequence. (B) Activities of the IS1 promoter::lacZ reporter construct (IS1) and the construct carrying site-specific mutations (-35M) were determined as described in Materials and Methods. The activity of the unaltered IS1 reporter was normalized to 1.0. (C) Results of RT-PCR with total IS1 RNA. The annealing sites for the primers used in the RT-PCR for each lane are shown in Fig. 1A. Lane 1, primers 16 and 17; lane 2, primers 16 and 20; lane 3, primers 19 and 17; lane 4, primers 18 and 17; lane 5, no-RT control with primers 16 and 17; lane 6, 100-bp DNA size standard ladder.
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FIG. 3. (A) Identification of cis-acting sequences that influence ltx operon expression in A. actinomycetemcomitans 652. The control construct, 652lacZ, contains the entire glyA-ltxC intergenic region fused to lacZ. Constructs IRL and IR20 were derived from 652lacZ and contain 20 random nucleotides separating the two segments of the IR and a deletion of the upstream segment of the IR, respectively. Deletion construct 229lacZ lacks the AT-rich IR and all additional sequences that reside upstream from the -35 element of Porf; construct 191lacZ contains the AT-rich sequence but lacks all other upstream sequences; construct 197lacZ contains only the portion of IR that resides downstream from the site of IS1301 insertion (see the text). The negative control, YGKlacZ, contains only a promoterless lacZ in the shuttle vector pYGK. For each construct, ß-galactosidase activity is shown on the right and was measured from cell extracts obtained from the recombinant strains by using ONPG as the substrate. (B) The AT-rich IR sequence resembles an UP element. The upper line represents the consensus UP element sequence (9), where W is A or T and N is any nucleotide; the lower sequence is the AT-rich IR element of the ltx promoter from A. actinomycetemcomitans 652 (Aa652). Homologous residues are indicated by colons; nucleotides that are analogous to the nonspecific residues in the consensus are indicated with X.
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Interaction of protein factors with the A. actinomycetemcomitans 652 promoter. To determine whether the IR or the upstream negative cis-acting region interacts with putative trans-acting proteins, oligonucleotide probes comprising nucleotides -77 to -166 (B101) and nucleotides -39 to -166 (B101IR) were reacted with a protein extract from A. actinomycetemcomitans 652 and analyzed by gel electrophoresis. These probes differ only in the presence of the IR sequence in the B101IR probe. A schematic representation of the glyA-orfA intergenic region and the probes used for mobility shift experiments is shown in Fig. 4A. Representative results from the mobility shift experiments using probes B101 and B101IR are shown in Fig. 4B and C, respectively. The mobility of each probe was retarded after incubation with the crude A. actinomycetemcomitans protein extract. Identical shifted probe bands were observed when the labeled probes were incubated with phosphocellulose chromatography-enriched protein extracts (data not shown). Interestingly, the addition of unlabeled B101 to these reaction mixtures as a competitive inhibitor (1.0, 2.5, and 5.0 M equivalents) inhibited the interaction of the protein factor(s) with both B101 and B101IR in a dose-dependent manner. This suggests that the upstream sequence, and not the IR itself, interacts with the polypeptide(s) in the cell extract. To further confirm that the mobility shift observed with probe B101IR (Fig. 4C) was not dependent upon the presence of the IR sequence, mobility shift experiments were carried out by using two additional probes that contained disrupted IR regions. Oligonucleotide probes B101IRL and B101IR20 were amplified by PCR from the plasmid constructs pIRL and pIR20 (Fig. 3A) and correspond to probe B101IR except that they contain a deletion and an insertion in the IR sequences, respectively. As shown in Fig. 4D, the mobility of all three probes (B101IR, B101IRL, and B101IR20) was retarded after incubation with the A. actinomycetemcomitans protein extract, suggesting that the interaction of the protein factor with these probes is independent of the IR. Together, these results suggest that the interaction of the putative trans-acting protein occurs only at the upstream cis-acting region.
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FIG. 4. (A) Schematic representation of the glyA-orfA intergenic region showing the probes used for mobility shift experiments. Probe B101IR contains the entire AT-rich IR sequence and extends from nucleotides -39 to -166, where +1 is the transcriptional initiation site of Porf. Probe B101 lacks the IR region and extends from -77 to -166. Probe B180 extends from -87 to -218, and probe B154 extends from -111 to -218. (B and C) For mobility shift experiments, 2 ng of biotinylated ltx promoter fragments B101 (B) and B101IR (C) was incubated with 7.5 µg of a protein extract derived from A. actinomycetemcomitans 652 and electrophoresed in 5% polyacrylamide gels. Competition experiments were carried out as described above in the presence of 2 to 10 ng of unlabeled B101 probe. Lanes 1, labeled probe; lanes 2, labeled probe and protein extract; lanes 3, labeled probe, extract, and 2 ng of unlabeled B101; lanes 4, labeled probe, extract, and 5 ng of unlabeled B101; lanes 5, labeled probe, extract, and 10 ng of unlabeled B101. (D) DNA probes B101IRL and B101IR20 correspond to B101IR but contain altered IR sequences. These probes were amplified from the recombinant plasmid constructs IRL and IR20 (Fig. 3). Biotinylated probes B101IR (lanes 1 to 4), B101IRL (lanes 5 to 8), and B101IR20 (lanes 9 to 12) were incubated with 7.5 µg of A. actinomycetemcomitans protein extract in the absence and presence of unlabeled B101IR probe (2 and 5 ng) and electrophoresed in 5% polyacrylamide gels. Lane 1, labeled B101IR; lane 2, B101IR and extract; lane 3, B101IR, extract, and 2 ng of unlabeled B101IR; lane 4, B101, extract, and 5 ng of unlabeled B101IR; lane 5, labeled B101IRL alone; lane 6, B101IRL and extract; lane 7, B101IRL, extract, and 2 ng of unlabeled B101IR; lane 8, B101IRL, extract, and 5 ng of unlabeled B101IR; lane 9, labeled B101IR20 alone; lane 10, B101IR20 and extract; lane 11, B101IR20, extract, and 2 ng of unlabeled B101IR; lane 12, B101IR20, extract, and 5 ng of unlabeled B101IR. (E) Probes B180 and B154 lack 10 and 36 bp, respectively, from the 3' end of probe B101. Biotinylated B180 and B154 were incubated with 30 µg of A. actinomycetemcomitans protein extract and electrophoresed in 5% polyacrylamide gels. Lane 1, labeled B154; lane 2, B154 and extract; lane 3, labeled B180; lane 4, B180 and extract.
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One mechanism whereby IS elements increase the expression of distal genes is by the introduction of an outwardly directed fusion promoter (6, 17, 34, 40, 47, 52, 54). Examination of the IS1301 sequence showed that it contains a sequence (TTGTAC) that resembles the consensus E. coli -35 promoter element in its downstream terminal repeat. Furthermore, in A. actinomycetemcomitans IS1, this putative -35 element resides 18 nucleotides upstream from the sequence AATAAT, which resembles the consensus -10 element (TATAAT). Thus, insertion of IS1301 may form a
70-like promoter upstream from the ltx operon. However, site-specific mutagenesis of this putative -35 sequence did not influence the transcriptional activity of the IS1 ltx promoter. In addition, RT-PCRs did not detect significant levels of ltx transcripts that are initiated upstream from the transcriptional initiation site of the orfA promoter (Porf). Thus, transcription of the ltx operon in strain IS1 does not appear to be driven by an IS1301 promoter. Therefore, the induction of ltx operon transcription must occur by an alternative mechanism such as the disruption by IS1301 of the normal transcriptional regulation of the operon.
Two cis-acting sequences that influence the expression of the ltx operon in A. actinomycetemcomitans 652 were identified in the ltx promoter region upstream from orfA (Porf). One of these sequences is an AT-rich imperfect IR that is located immediately upstream from the -35 sequence in Porf. Deletion or alteration of this sequence led to decreased transcriptional activity of Porf, suggesting that the AT-rich IR functions as a positive regulator of leukotoxin expression. Indeed, the structural and functional characteristics of this sequence resemble those of an UP element. UP elements are positive cis-acting AT-rich sequences that are usually located immediately upstream from the -35 promoter element and stimulate transcription by interacting with the ß-subunit of RNA polymerase (7, 9, 43). The AT-rich IR is homologous to the consensus UP element sequence (9) in 19 of 22 positions. Functional experiments are currently under way to determine whether the ß-subunit of A. actinomycetemcomitans RNA polymerase interacts with the AT-rich IR in Porf. The second cis-acting regulatory region identified in our studies resides upstream from the putative UP element in A. actinomycetemcomitans 652. Deletion of this region resulted in a fourfold increase in the transcriptional activity of Porf, indicating that this sequence functions to down regulate leukotoxin expression. Furthermore, mobility shift experiments showed that this region interacts with a protein factor(s) in extracts from A. actinomycetemcomitans 652 and that nucleotides -87 to -111 (Fig. 4) are required for this interaction to occur. The nature of this polypeptide and the mechanism by which it regulates leukotoxin expression are not known; studies to isolate and identify the putative trans-acting regulator are ongoing. Interestingly, the interaction of the protein factor with B101IR was inhibited more effectively with unlabeled B101 (Fig. 4, compare panels B and C). The reason for this is not clear. However, AT-rich sequences are known to promote stable bends in DNA (39) and it is possible that the AT-rich IR forms a secondary structure that sterically inhibits protein interactions with the upstream sequence in probe B101IR.
The positions of the two cis-acting regulators relative to the site of IS1301 insertion suggest a possible mechanism that may contribute to the hyperleukotoxic phenotype exhibited by A. actinomycetemcomitans IS1. In strain IS1, IS1301 is integrated into the upstream portion of the AT-rich IR, at nucleotide -71. The surrounding sequence, ACTAA, closely resembles the reported target integration sequence (AYTAG, where Y represents pyrimidine) for IS1301 in N. meningitidis strains (16). Thus, the acquisition of IS1301 displaces 6 nucleotides of the AT-rich IR (residues -71 to -77) and the putative negative cis-acting sequence (nucleotides -87 to -111) approximately 900 bp upstream from the basal promoter elements of Porf. Our results show that deletion of nucleotides -71 to -79 (clone 197lacZ) did not affect the transcriptional activity of Porf reporter constructs. In contrast, deleting the portion of the AT-rich sequence that resides downstream from the site of IS1301 insertion (clone 229lacZ) significantly reduced transcriptional activity. Thus, the acquisition of IS1301 has little effect on transcriptional stimulation of the ltx operon mediated by the putative UP element. Our results suggest that, in the absence of an IS1301 promoter, the hyperleukotoxic phenotype arises at least in part from the displacement of the negative cis-acting element by IS1301. The uncoupling of negative regulation may therefore allow the ltx operon of strain IS1 to be predominantly controlled by the positive cis-acting element, leading to increased overall expression of leukotoxin. It is also possible that IS1301 possesses additional positive cis-acting regions that stimulate the transcriptional activity of Porf.
The insertion and excision of IS1301 in siaA of N. meningitidis have been reported to function as a reversible genetic switch that controls the biosynthesis of sialic acid (11). This switch regulates capsule expression and lipo-oligosaccharide sialylation which in turn controls the bacterium's adherence to and invasiveness in mucosal epithelial cells (11). Reversible IS-mediated regulation of gene expression has also been reported in Pseudomonas aeruginosa PAO (49) and Pseudomonas atlantica (1). The excision and reinsertion of IS elements at defined sites in the genome suggest that the transposase exhibits a high degree of specificity in recognizing the specific target sequence. Indeed, IS1301 integrates at a defined target sequence (see above) and also requires additional structural features, e.g., extended palindromic symmetry, stem-loop formation, and the presence of AT-rich tracts (16). All of these features are conserved at the site of IS1301 integration into A. actinomycetemcomitans IS1. While the frequency of excision and reinsertion of IS1301 upstream from the ltx operon in A. actinomycetemcomitans is not currently known, it is tempting to speculate that a similar reversible genetic switch may regulate the expression of leukotoxin. The resulting flux in leukotoxin expression may therefore influence virulence of A. actinomycetemcomitans and contribute to the periodic nature of periodontal disease.
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