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J Bacteriol. Jul 2008; 190(13): 4736–4748.
Published online May 2, 2008. doi:  10.1128/JB.00089-08
PMCID: PMC2446820

Integration Host Factor Positively Regulates Virulence Gene Expression in Vibrio cholerae[down-pointing small open triangle]

Abstract

Virulence gene expression in Vibrio cholerae is dependent upon a complex transcriptional cascade that is influenced by both specific and global regulators in response to environmental stimuli. Here, we report that the global regulator integration host factor (IHF) positively affects virulence gene expression in V. cholerae. Inactivation of ihfA and ihfB, the genes encoding the IHF subunits, decreased the expression levels of the two main virulence factors tcpA and ctx and prevented toxin-coregulated pilus and cholera toxin production. IHF was found to directly bind to and bend the tcpA promoter region at an IHF consensus site centered at position −162 by using gel mobility shift assays and DNase I footprinting experiments. Deletion or mutation of the tcpA IHF consensus site resulted in the loss of IHF binding and additionally disrupted the binding of the repressor H-NS. DNase I footprinting revealed that H-NS protection overlaps with both the IHF and the ToxT binding sites at the tcpA promoter. In addition, disruption of ihfA in an hns or toxT mutant background had no effect on tcpA expression. These results suggest that IHF may function at the tcpA promoter to alleviate H-NS repression.

The ability of pathogenic bacteria to modulate the expression of genes in response to environmental stimuli is widespread and critical for bacterial survival within specific niches. Nucleoid-associated proteins, such as H-NS, integration host factor (IHF), Fis, and HU play important roles in this adaptive process. These proteins comprise a group of abundant DNA-binding proteins that condense the bacterial chromosome, modulating its structure and influencing many cellular processes, such as DNA replication (51), site-specific recombination (5, 16), and transcription (35). The nucleoprotein complexes formed in response to environmental cues have both negative and positive influences on transcription, and these proteins function with one another and with gene-specific regulatory factors to fine tune gene expression.

The nucleoid-associated protein H-NS is an abundant global regulator that influences various cellular processes (13, 14, 41). H-NS binds DNA with relatively low sequence specificity but instead has a preference for AT-rich segments with intrinsic planar curvature (49, 68). Studies using chromatin immunoprecipitation-on-chip technology have identified the H-NS binding regions over the Escherichia coli and Salmonella enterica serovar Typhimurium genomes (18, 32, 42, 44). Their results demonstrate that H-NS binds to regions of high AT content, including genes acquired by horizontal gene transfer. Of interest was the finding that H-NS interacts with extensive DNA stretches on pathogenicity islands and represses the transcription of the associated virulence genes. This discovery has raised speculation that H-NS may function to silence foreign DNA until dedicated transcription factors are able to relieve H-NS repression (14). Recent studies have proposed that H-NS dimers bind to nucleating high-affinity sites, corresponding with the identified 10-bp consensus motif TCGATAAATT, located within AT-rich regions, and polymerize outward along the DNA, eventually resulting in the condensation of DNA through the formation of protein bridges between H-NS binding sites (4, 29). This DNA remodeling can directly interfere with RNA polymerase action or block the binding of specific activators at a nearby promoter region.

IHF is a heterodimeric protein composed of the subunits IHFα (11.3 kDa) and IHFβ (10.6 kDa), encoded by the ihfA (himA) and ihfB (hipB) genes, respectively. The two subunits have approximately 35% identity to each other. Unlike H-NS, IHF recognizes a specific asymmetric site on DNA, the 13-bp consensus target sequence WATCAANNNNTTR, where W represents A or T and R represents A or G (10). Upon binding, IHF is known to bend DNA by as much as 180° (48, 61). In E. coli and S. enterica serovar Typhimurium, IHF is involved in controlling the transcriptions of over 100 genes of various functions (2, 33, 35). In addition, IHF has increasingly been identified as a regulator of virulence gene expression in various pathogens. IHF is required for appropriate expression of the Brucella abortus virB operon, encoding the type IV secretion system (52). In Shigella flexneri, IHF positively regulates virulence gene expression at multiple promoters, including the virF, virB, and icsA promoters (47). Flagellum production in enteropathogenic and enterohemorrhagic E. coli strains is repressed by IHF (69). IHF can act as a transcriptional regulator by different mechanisms. In several cases, IHF produces a DNA bend that enables the direct interaction of a distant, DNA-bound transcriptional regulator with RNA polymerase to enhance transcription (15). DNA bending by IHF can stimulate the recruitment of RNA polymerase to activate transcription by favoring the interaction of the α subunit C-terminal domain with upstream DNA UP elements (3). IHF binding can also serve to lower the activation energy for open complex formation (45). IHF typically acts as an architectural factor that leads to the correct promoter structure necessary for transcriptional regulation. An alternative mechanism of IHF activation is antirepression of H-NS-repressed promoters (63).

Virulence gene expression in the human enteric pathogen Vibrio cholerae is dependent upon a complex transcriptional cascade that is influenced by both specific regulators, such as ToxR/S, TcpP/H, and ToxT, and global regulators, such as cyclic AMP-cyclic AMP receptor protein and H-NS, in response to environmental stimuli (for reviews, see references 9 and 55). Production of the two main virulence factors, the toxin-coregulated pilus (TCP) (60) and the cholera toxin (CT) (23), is required for human colonization and causes the severe watery diarrhea that is characteristic of the disease. Both of these virulence factors are carried on genetic elements acquired by horizontal gene transfer that have a higher AT content (>60% AT rich) than the ancestral chromosome (52% AT rich). The tcp genes are carried on the Vibrio pathogenicity island (VPI), and the ctx genes are carried on the CT phage. The expression of the tcp and ctx genes is transcriptionally controlled in response to environmental stimuli by a regulatory cascade, termed the ToxR virulence regulon, that involves proteins encoded within both the ancestral Vibrio genome and the VPI. The cascade is initiated by two chromosomally encoded proteins, AphA and AphB, functioning synergistically to activate transcription of tcpPH (25, 56). TcpP and TcpH (6, 20) are transmembrane proteins encoded on the VPI that, along with a second pair of transmembrane proteins, ToxR and ToxS (37, 38), activate transcription at the toxT promoter in a cooperative manner (21, 28). ToxT directly activates the expression of many genes, including the tcp operon (7, 12, 22, 71), the ctx operon (12), and the accessory colonization factor genes acfA and acfD (46, 65). In addition, ToxT autoregulates its own expression through activation of the tcpA promoter and readthrough into toxT (70).

In addition to the specific regulatory proteins of the ToxR virulence regulon mentioned above, the nucleoid-associated protein H-NS has been shown to play an important role in V. cholerae virulence gene expression (17, 27, 43). Mutation of V. cholerae hns causes derepression of toxT, tcpA, and ctx expression to near-wild-type levels even in the absence of cognate activator proteins (43). A variety of data indicate that H-NS directly influences transcription at each of these promoters. Thus, H-NS functions at multiple promoters within the cascade to reduce virulence gene expression under particular environmental conditions.

In the present study, we show that, in contrast to H-NS, the nucleoid protein IHF positively influences virulence gene expression in V. cholerae. Deletion of either the ihfA or the ihfB gene decreased chromosomally encoded ctx-lacZ and tcpA-lacZ promoter fusion expression and prevented TCP and CT production. The same mutations had no effect on tcpP-lacZ or toxT-lacZ fusions. Gel mobility shift assays and DNase I footprinting experiments with purified V. cholerae IHF demonstrate that IHF recognizes a putative IHF consensus site within the tcpA promoter and introduces a bend upon binding. DNase I footprinting at tcpA revealed that H-NS binding covers the identified IHF consensus site as well as the ToxT site. In addition, we determined that the dependence on IHF for optimal tcpA expression requires the presence of both H-NS and ToxT.

MATERIALS AND METHODS

Bacterial strains and growth.

The V. cholerae and E. coli strains and plasmids used in this study are listed in Table Table1.1. Strains were maintained at −70°C in Luria-Bertani (LB) medium (36) containing 30% (vol/vol) glycerol. Antibiotics were used at the following concentrations in LB medium: ampicillin (Amp), 100 μg/ml; gentamicin, 30 μg/ml; kanamycin (Kan), 45 μg/ml; polymyxin B, 50 IU/ml; and streptomycin, 1 mg/ml. 5-Bromo-4-chloro-3-indolyl-β-d-galactopyranoside (X-Gal) was used in LB agar at 40 μg/ml (Sigma).

TABLE 1.
Bacterial stains and plasmids used in this study

Construction of chromosomal ihf deletions.

The ihfA subunit deletion was constructed in pKAS32 (53) by PCR using primer HMEco (oligonucleotide sequences are listed in Table Table2)2) with HMNot1 and HMNot2 with HMXba. A Kanr fragment was inserted between the two fragments at the NotI site, and the resulting plasmid, pGKK158, was used for allelic exchange. The ihfB subunit deletion construct was created in pKAS46 (53) by PCR using primer HBEco with HBNotI and primer HBNot2 with HBXba. A Genr fragment was inserted between the two fragments at the NotI site, and the resulting plasmid, pGKK162, was used for allelic exchange. Deletions were confirmed by PCR.

TABLE 2.
Oligonucleotides used in this study

Expression plasmids.

Plasmid pKAS161 was constructed by PCR amplifying a 1-kb fragment containing the ihfA subunit with primers HMEco and HMXba. The resulting product was directly cloned into pBAD-TOPO (Invitrogen) and sequenced.

The V. cholerae hns expression plasmid pEAS10 was constructed by PCR amplifying the 414-bp hns gene from O395 chromosomal DNA by using HNS1 and HNS2. The resulting fragment was digested with NdeI and SapI and ligated into similarly cut pTXB-1 to generate pEAS10. The nucleotide sequence was confirmed by DNA sequencing.

Construction of IHF binding site mutations.

The 21-bp deletion of the putative IHF consensus site in the tcpA promoter was constructed using primer pairs H-Eco/Sap1B and ABgl2/Ear1T to amplify chromosomal sequences from O395. The fragments were digested with SapI and EarI to produce seamless junctions, followed by BglII and EcoRI digestion and ligation into pKAS32 to generate pEAS9. The resulting plasmid was confirmed by sequencing. To construct four base pair mutations (shown in Fig. Fig.4C)4C) in the most highly conserved residues of the IHF consensus site, the primer pairs H-Eco/Sap2B and Ear3T/ABgl2 were used to amplify O395 chromosomal DNA. After digestion as described above, the fragments were ligated into pKAS32, generating p4PM-tcpA, and sequenced. These mutations were introduced into the tcpA-lacZ fusion strain (MBN135) or O395 by allelic exchange and subsequently confirmed by sequencing.

FIG. 4.
DNase I protection by IHF and H-NS at the tcpA promoter. The top and bottom strands of the tcpA promoter fragments were incubated with increasing amounts of IHF (1.2 and 2.4 μM) (A) or H-NS (1, 2, and 4 μM) (B) and treated with DNase I. ...

β-Galactosidase assays.

β-Galactosidase assays (36) were carried out after overnight growth in LB medium with a starting pH of 6.5 at 30°C and shaking. Due to TCP-mediated bacterial autoagglutination, the specific activities of strains in the ctx-lacZ background were calculated using the protein concentration determined by a bicinchoninic acid procedure (Pierce) rather than using the more standard optical density normalization method.

CT assays.

GM1 ganglioside enzyme-linked immunosorbent CT assays (23) were carried out on the supernatants of overnight cultures grown in LB medium with a starting pH of 6.5 at 30°C and shaking.

Immunoblot analysis.

Whole-cell protein extracts prepared from the overnight cultures used for CT assays were subjected to sodium dodecyl sulfate-12.5% polyacrylamide gel electrophoresis, transferred to a nitrocellulose membrane, probed with an anti-TcpA antibody (59) or an anti-ToxT polyclonal antibody, and visualized using an enhanced chemiluminescence detection system (Amersham).

Purification of the V. cholerae IHF heterodimer.

Plasmids pEAS2 and pEAS3 were generated to overexpress the genes encoding the IHFα and IHFβ subunits, respectively. The ihfA gene was amplified from O395 chromosomal DNA by using primers ihfA1 and ihfA2, digested with EcoRI and SphI, and ligated into similarly cut pBAD22, creating pEAS2. The ihfB gene was amplified from O395 chromosomal DNA with the primer pair ihfB1/ihfB2, digested with EcoRI and SphI, and ligated into pEAS1, creating pEAS3. pEAS1 was generated by ligating the 50-bp ribosomal binding site from pBAD22 (NheI/SphI-digested fragment) into pKAS178 (a pBAD33 Kmr derivative) to replace the pBAD33 ribosomal binding site. This ensured that the translational efficiencies of ihfB from pEAS3 and ihfA from pEAS2 were comparable. The nucleotide sequences of both constructs were confirmed by sequencing. V. cholerae O395 harboring both pEAS2 and pEAS3 was grown overnight in 10 ml of LB at 37°C with shaking and used to inoculate 2 liters of LB containing Amp/Kan. The culture was grown for 3 h, and arabinose was then added to give a final concentration of 0.1%. Following overnight incubation at 37°C with shaking, the V. cholerae IHF heterodimer was extracted as soluble protein as previously described (40). Briefly, the culture was centrifuged, sonicated, and recentrifuged and the supernatant was precipitated with 50% ammonium sulfate. After centrifugation, the resulting supernatant was precipitated with 70% ammonium sulfate and the pellet was resuspended in 1 ml of TG (50 mM Tris [pH 7.4], 10% glycerol) containing 10 mM KCl. The protein was then dialyzed overnight against TG containing 10 mM KCl, loaded onto a phosphocellulose column, and eluted with a KCl salt gradient from 10 mM to 1.2 M in TG. The IHF-containing fractions were pooled, dialyzed against a 25 mM NaH2PO4 (pH 5.5), 1 mM EDTA, 5% glycerol buffer, fractionated over a cation exchange Macro-Prep High S support (Bio-Rad) at pH 5.5, and developed with a linear gradient (75 to 800 mM) of NaCl in 25 mM NaH2PO4 buffer. The fractions were analyzed on an 18% urea polyacrylamide gel, and the IHF-containing fractions were pooled and further dialyzed against 25 mM NaH2PO4, 1 mM EDTA, 5% glycerol. The estimated purity of the IHF heterodimer was 95% as determined by densitometry.

Purification of V. cholerae H-NS.

H-NS was purified using the IMPACT-CN system, which uses a cleavable chitin binding domain fused to the C terminus of a protein for purification utilizing a chitin column (New England Biolabs). E. coli strain ER2566, containing the hns expression plasmid pEAS10, was grown in LB containing Amp at 37°C for 3 h, induced with 1 mM IPTG (isopropyl-β-d-thiogalactopyranoside), and grown overnight at 16°C. The cells were collected by centrifugation and resuspended in column buffer (20 mM Tris [pH 8.0], 500 mM NaCl, 1 mM EDTA). The extract was sonicated and clarified by centrifugation at 14,000 rpm for 30 min in an SS34 rotor. The supernatant was then loaded onto a chitin column equilibrated with column buffer to bind the fusion protein and washed with 10 volumes of column buffer and high-salt column buffer (containing 1 M NaCl). Three volumes of cleavage buffer (column buffer containing 100 mM dithiothreitol [DTT]) were added, and the column was incubated overnight at 4°C. H-NS was then eluted off the column with column buffer. The eluted protein was dialyzed overnight in a solution of 20 mM Tris (pH 8.0), 1 mM EDTA, 5 mM potassium glutamate, and 0.1 mM DTT. Glycerol was added to the protein to 10%, and the protein was stored at −70°C. The final purity of H-NS was estimated to be greater than 90% as determined by densitometry.

Gel mobility shift assays.

DNA fragments containing the putative IHF binding sites in the promoter regions of the tcpA and ctx operons were generated by PCR from V. cholerae O395 chromosomal DNA or from the pEAS9 or p4PM-tcpA plasmid with the TCP-SAL (−226)/TCP-XHO (+78), TCP-SAL/tcp2 (−50), tcp1 (−100)/TCP-XHO, or ctxP2 (−194)/ctxP1 (+118) oligonucleotide pair. IHF gel mobility shift assays were carried out in a volume of 20 μl containing DNA-binding buffer (50 mM Tris [pH 7.4], 70 mM KCl, 1 mM EDTA, 1 mM DTT, 100 μg/ml bovine serum albumin, 5% glycerol), 10 ng of digoxigenin (DIG)-labeled DNA, 1.5 μg of calf thymus DNA, and purified IHF heterodimers. After incubation at 30°C for 15 min, protein-DNA complexes were separated from free probes by electrophoresis on 5% nondenaturing polyacrylamide gels and transferred to nylon. H-NS gel mobility shift assays were carried out in a volume of 20 μl containing DNA-binding buffer (40 mM HEPES, 100 mM potassium glutamate, 10 mM magnesium aspartate, 0.022% NP-40, 100 μg/ml bovine serum albumin, 10% glycerol), 10 ng of DIG-labeled DNA, 1 μg of calf thymus DNA, and purified H-NS. After incubation at room temperature for 20 min, protein-DNA complexes were separated by 5% nondenaturing polyacrylamide gel electrophoresis and transferred to nylon. DNA was visualized with an anti-DIG detection kit (Roche), followed by enhanced chemiluminescence detection.

DNase I footprinting.

DNA fragments of 232 and 360 bp were generated from the O395 tcpA promoter by amplification with the tcp7 (−282)/tcp2 (−50) or tcp7/tcp9 (+78) primer pair. These fragments were ligated into pBlueScript (Stratagene), generating pEAS4 and pEAS5, respectively. Fragments for labeling were digested from pEAS4 and pEAS5 with EcoRI and BamHI. Strand labeling was carried out essentially as described by Kovacikova and Skorupski (26). Binding reactions were performed in a 6.5-μl volume containing 33P-end-labeled DNA, purified IHF or H-NS, and the corresponding binding buffer as described above. After incubation at 30°C for 15 min, protein-DNA complexes were digested with 1 μl of various dilutions of DNase I (Promega) for 5 min at 30°C. The reactions were stopped by addition of 2 mM EGTA, followed by heat inactivation at 65°C for 10 min and then spot dialysis for 30 min against 10 mM Tris (pH 8.0), 0.1 mM EDTA. The reaction mixtures were then heated to 90°C for 5 min in formamide loading buffer (Epicenter) and separated on a 6% acrylamide sequencing gel with 1× Tris-borate-EDTA. The gels were dried and visualized by autoradiography.

Circular permutation assay.

The ability of IHF to bend DNA at its binding site was tested as described by Wu and Crothers (66). A 67-bp fragment containing the IHF binding site was amplified with primers tcp12 and tcp13 and cloned into the HpaI site of pBEND5 (72), generating pEAS7. The insert was confirmed by sequencing. Permutated DNA fragments were generated from pEAS7 by digestion with the enzymes listed in Fig. Fig.5,5, and the resulting 190-bp fragments were purified from polyacrylamide gels and labeled with DIG. A standard gel mobility shift assay with purified IHF was performed on each fragment as described above.

FIG. 5.
Bending of the tcpA promoter DNA by IHF as determined by a circular permutation assay. (A) Diagram of 190-bp linear probes produced by digestion of plasmid pEAS7 (pBEND5-tcpA) with five restriction enzymes. The probes contain the IHF consensus site (hatched ...

RESULTS

IHF positively regulates expression of the tcpA and ctx promoters.

To assess the influence of IHF on the regulation of virulence gene expression in V. cholerae, ΔihfA::kan and ΔihfB::gen mutants were constructed in the ctx-lacZ fusion strain KSK218 (54). Under conditions known to induce virulence gene expression, LB with a starting pH of 6.5 at 30°C, both ihf mutants showed fivefold reductions in ctx-lacZ expression (Fig. (Fig.1A).1A). Since tcpA expression is coordinate with that of ctx, the influence of the ihf mutations on a tcpA-lacZ fusion strain, MBN135 (43), was assessed and expression was also reduced approximately fourfold (Fig. (Fig.1A).1A). These results show that IHF plays a role in the positive activations of the ctx and tcpA promoters. Expression of the α subunit of IHF in pBAD-TOPO (pKAS161) in the ihfA mutant strain restored normal ctx-lacZ and tcpA-lacZ expression, confirming that the decreased expression levels observed at these promoters were due to the lack of functional IHF in the ΔihfA::kan strain (Fig. (Fig.1B1B).

FIG. 1.
Influence of IHF on ctx-lacZ and tcpA-lacZ expression. (A) Wild-type (WT) (tcpA-lacZ or ctx-lacZ), ihfAihfA::kan), or ihfBihfB::gen) mutants. (B) WT, ihfA, or ihfA mutants with the empty vector pBAD-TOPO or the IHFα expression ...

Introduction of the ΔihfA::kan mutation into wild-type O395 confirmed that the production of TCP and CT in V. cholerae is dependent upon IHF. As observed in Fig. Fig.2A,2A, the ΔihfA::kan mutant ES21 is considerably reduced for TcpA and CT production when grown under inducing conditions. In addition, both of these products were restored with ihfA overexpression from pEAS2 (Fig. (Fig.2A2A).

FIG. 2.
TcpA, CT, and ToxT production in O395 and the ihfA mutant. Strains were grown overnight in LB medium with a starting pH of 6.5 at 30°C with shaking. Western blot analysis with the anti-TcpA (α-TcpA) antibody (A) or α-ToxT polyclonal ...

The influence of IHF on virulence gene expression could be the result of a direct effect at the ctx and tcpA promoters, or the effect could be indirect due to an influence of IHF at promoters further upstream in the virulence cascade, such as the tcpPH, toxR, or toxT promoter. To address the IHF effect on tcpPH, the ΔihfA::kan and ΔihfB::gen mutations were introduced into the tcpPH-lacZ strain KSK618 (56). The expression of tcpPH was not influenced by either ihf mutation (data not shown). Levels of ToxR, a member of the protein pair that cooperates with TcpP/H to activate toxT expression, were also unaffected by the ΔihfA::kan mutation, as detected by immunoblot analysis (data not shown). The expression of toxT is influenced by two promoters, one that is TcpP/ToxR dependent, located immediately upstream of toxT, and one that is ToxT dependent and initiates upstream of tcpA (see Fig. Fig.8).8). To determine the effect of IHF on toxT expression from the TcpP/ToxR-dependent promoter, the ΔihfA::kan and ΔihfB::gen mutations were introduced into the toxT-lacZ strain MBN032, which is lacking ToxT (43). Expression from this promoter was not influenced by either ihf mutation (data not shown). To address whether IHF influences toxT expression from the ToxT-dependent promoter upstream of tcpA, a Western blot analysis was performed to assess whether total ToxT levels were altered in the ihfA mutant. As shown in Fig. Fig.2B,2B, ToxT levels were lower in the ihfA mutant than in the wild type upon growth to late log phase under inducing conditions. Additionally, when total toxT transcript from nonfusion backgrounds was measured by quantitative real-time PCR from cultures grown overnight under inducing conditions, toxT transcript levels were decreased similarly to tcpA transcript levels in the ihfA mutant compared to wild-type levels (data not shown). The observation that IHF does not appear to influence expression from the TcpP/ToxR-dependent promoter and yet total transcript levels (TcpP/ToxR-dependent and ToxT-dependent toxT transcripts) were reduced in the ihfA mutant suggests that IHF might have a direct effect on the ToxT-dependent promoter upstream of tcpA. The decreases in ctx expression and CT production in this mutant are most likely due to reduced toxT expression resulting from the influence of IHF at the tcpA promoter. This is further supported by studies of IHF binding at these promoters (see below).

FIG. 8.
Schematic of the transcriptional regulation of V. cholerae tcpA, toxT, and ctx expression. (A) OFF/INITIAL: H-NS represses gene expression at multiple promoters within the ToxR regulon, including tcpA to -F, toxT, and ctx. H-NS binding in the tcpA promoter ...

Purified IHF from V. cholerae binds the tcpA promoter region between positions −226 and −50.

Gel mobility shift assays were used to assess whether IHF directly binds to the virulence gene promoter regions. Increasing amounts of purified V. cholerae IHF (180 and 360 nM) were incubated with 10 ng of ctx (C) or tcpA (A1) promoter fragments. IHF did not bind the ctx fragment (C) but did bind the tcpA fragment (A1) (Fig. (Fig.3),3), suggesting a direct role for IHF at the tcpA promoter and not the ctx promoter. tcpP and toxT promoter fragments also failed to bind IHF in gel mobility shift assays (data not shown). These results are consistent with expression data that suggest that IHF does not have a direct regulatory role at the tcpP or toxT promoters.

FIG. 3.
Gel mobility shift assay for IHF binding to ctx and tcpA promoter DNA. The DIG-labeled promoter fragments of ctx from position −194 to +118 (C) and tcpA from position −226 to +78 (A1), −226 to −50 (A2), ...

To locate the IHF binding site within the tcpA promoter region, smaller fragments (A2 and A3) were used to determine where binding occurs. Two putative IHF consensus sites based on the E. coli IHF consensus site WATCAANNNNTTR, where W represents A or T and R represents A or G, are present within the tcpA promoter. One site overlaps the −35 region (5′-CATCTGTCAATTG), while the second is located upstream and centered at position −162 (5′-AATCATTTGAATT), about 80 bp upstream of the ToxT binding site (positions −84 to −41). IHF was capable of binding to the promoter fragment containing the −162 site alone (−226 to −50) (A2), whereas it was not capable of binding to the −35 site alone (−100 to +78) (A3) (Fig. (Fig.3).3). Despite the presence of only one shifted complex on the A1 fragment containing both putative sites, it is formally possible that IHF binds the −35 site only in the presence of the −162 site. This possibility was examined in DNase I footprinting experiments where both sites were present on the same fragment (see below). Notably, the DNA surrounding the −162 site from position −200 to −125 has 76% AT content. The high AT content, coupled with the knowledge that the nucleoid-associated protein H-NS directly represses tcpA expression (71) and itself preferentially binds AT-rich DNA (18, 32, 42, 44), suggests that the region around position −162 may also be an H-NS binding site. Scanning of this region for putative H-NS nucleation sites by use of the 10-bp consensus site identified by Lang et al. (29) revealed two matches adjacent to the IHF consensus site (Fig. (Fig.4C,4C, boxes), further suggesting that IHF and H-NS could both bind this region of the tcpA promoter.

IHF and H-NS binding sites overlap the −162 IHF consensus site.

DNase I footprinting was used to determine if IHF and H-NS bind the same −162 region within the tcpA promoter. Radiolabeled fragments that spanned the tcpA promoter region from position −282 to −50 (IHF footprint) and from position −282 to +78 (H-NS footprint) were generated, incubated with increasing amounts of IHF (1.2 μM and 2.4 μM) and H-NS (1 μM, 2 μM, and 4 μM), respectively, and digested with DNase I as described in Materials and Methods. The reaction mixtures were then subjected to electrophoresis on a denaturing polyacrylamide gel. IHF protected a region from position −185 to −126 on the top strand and a region from position −198 to −136 on the bottom strand (Fig. (Fig.4A).4A). This protection overlapped the putative IHF consensus site at position −162 and the two putative H-NS nucleation sites, as shown in Fig. Fig.4C.4C. DNase I-hypersensitive sites, a characteristic of DNA bending, flank the IHF protection, suggesting that IHF might be bending the tcpA promoter upon binding. IHF did not protect the putative IHF consensus site at the −35 site on the longer (−282 to +78) tcpA fragment that contained both IHF consensus sites (data not shown). This suggests that the putative IHF site at position −35 is not bound by IHF even in the presence of the −162 site and that the single shifted complex observed with the A1 fragment in Fig. Fig.33 is IHF binding to the −162 site alone.

H-NS binding was more widespread than IHF binding within the tcpA promoter region. H-NS bound over the IHF binding site at position −162 and strongly protected at least part of the ToxT binding site that spans from position −84 to −41 in the promoter region (71) (Fig. (Fig.4B).4B). This binding region has an AT content >70% similar to that of the IHF binding region. These results suggest that H-NS binding overlaps the binding sites of both activators, IHF and ToxT, at the tcpA promoter and could act to block the binding of these activator proteins.

IHF binding induces bending of the DNA upstream of tcpA.

IHF has been shown to bend DNA in a number of systems (61), and this property has been suggested to be central to its activities (39, 50, 57). We used the circular permutation assay of Wu and Crothers (66) to determine the ability of IHF to bend 190-bp restriction fragments containing a 67-bp fragment of the tcpA promoter region encompassing the IHF binding site at different positions relative to the ends of the restriction fragment, as shown in Fig. Fig.5A.5A. The bending assay is based on the observation that differences exist in the migration of linear and bent DNA fragments and that the electrophoretic mobility of bent protein-bound DNA differs with the positioning of the DNA-binding site relative to either end of the fragment. The more centrally located the bending site, the more retarded the migration of the protein-DNA complex. Gel mobility shift assays with each fragment in the presence of IHF were carried out as described above. All free DNA migrated at the same rate, suggesting that there was no intrinsic bend in the DNA. Mobility upon incubation with IHF was slowest when the IHF binding site was centrally located (EcoRV) and maximal when the site was closest to the end of the fragment (BglII and BamHI). These results are consistent with the center of the bend being located at the IHF binding site. Migration of the fragments bound by IHF was measured from the well, and the bending angle was calculated to be 120° by the method of Thompson and Landy (61).

The influence of IHF consensus site mutations on IHF binding and tcpA expression.

The IHF consensus site was altered in order to disrupt IHF binding and activity at the tcpA promoter. The first binding site mutation, termed Δconsensus, was a 21-bp deletion that included the 13-bp IHF consensus site (Fig. (Fig.4C).4C). The second, termed 4PM, was the introduction of 4-base-pair changes in the most highly conserved consensus site residues, in which the TCA and the second-to-last T were changed to GGT and G, respectively (Fig. (Fig.4C).4C). Fragments of the tcpA promoter region from position −226 to +78 containing these mutations were assessed for their effects on IHF binding in gel mobility shift assays as described above. IHF did not shift fragments containing the Δconsensus or the 4PM mutation (Fig. (Fig.6A).6A). These results suggest that this site is essential for IHF binding. These mutations were then assayed for their effects on tcpA transcription by integration into the tcpA-lacZ background. Contrary to what was expected, neither the Δconsensus nor the 4PM mutation mimicked an ihf mutant in its effect on tcpA expression. Rather than the 4-fold decrease seen previously in the ihf mutants, the promoter IHF consensus mutations caused only a 1.6-fold decrease in tcpA-lacZ expression (data not shown). In addition, TcpA protein production was similar to wild-type levels when these mutations were placed in the otherwise wild-type O395 background (data not shown). This result suggests that the mechanism of IHF activation at this site may be more complicated than simply binding to the IHF consensus site.

FIG. 6.
Mutations in the tcpA IHF consensus site alter IHF and H-NS binding. Mutations in the tcpA promoter were constructed to disrupt IHF binding. The wild-type (WT) and mutant promoter fragments (Δconsensus and 4PM) from position −226 to +78 ...

H-NS binding to the IHF consensus mutations in gel mobility shift assays.

One of the mechanisms by which IHF can regulate transcription is alleviation of H-NS-mediated repression of transcription (63, 64). Based on the idea that IHF can act as an antirepressor and given the DNase I protection data that show overlapping H-NS and IHF sites, we chose to investigate whether the IHF consensus site mutations affected H-NS binding to the tcpA promoter fragments. Gel mobility shift assays were performed with wild-type and mutant tcpA promoter fragments from position −226 to +78 with increasing amounts of H-NS (Fig. (Fig.6B).6B). At low concentrations of H-NS, two shifted bands occurred with the wild-type fragment, a result consistent with our DNase I protection determination that showed multiple H-NS binding sites within this promoter region. The wild-type fragment was completely shifted in the presence of 320 nM H-NS, whereas fragments containing the Δconsensus and 4PM mutations were not fully shifted at 320 nM H-NS. These results suggest that the IHF consensus site within the tcpA promoter not only is critical for IHF binding but also contributes to optimal H-NS binding. The reduced H-NS binding in the Δconsensus and 4PM mutants may thereby serve to decrease repression of the tcpA promoter and partially alleviate the requirement for IHF. The Δconsensus promoter mutation deletes 5 of the 10 bp that comprise the second putative H-NS high-affinity nucleation site (Fig. (Fig.4C)4C) and could function to disrupt H-NS nucleation and polymerization from this site.

Competitive gel mobility shift assays were performed between IHF and H-NS on the tcpA promoter region to examine the effect of adding either protein to prebound DNA complexes of the other. The DNA was incubated with the lowest concentrations of H-NS or IHF (320 or 420 nM, respectively) that gave a complete shift of the free DNA. After 15 min at 30°C, increasing amounts of IHF or H-NS, respectively, were added and incubation was continued for an additional 15 min. Addition of either 120 or 240 nM of IHF to a prebound H-NS fragment did not influence H-NS binding. However, addition of 420 nM IHF resulted in displacement of H-NS from the DNA and a shift to a predominately IHF-DNA complex. Addition of 160 to 320 nM H-NS to a prebound IHF-DNA fragment did not significantly influence the IHF-DNA complex. These results suggest that IHF effectively displaces H-NS from the tcpA promoter fragment and that, once bound, IHF can essentially prevent H-NS binding.

Interplay of IHF, H-NS, and ToxT in the regulation of tcpA expression.

It is known that H-NS represses tcpA transcription. It has been shown that IHF alleviates H-NS repression at the bacteriophage Mu early (Pe) promoter and at the virB promoter in Shigella flexneri (47, 63). In an attempt to establish whether IHF functions as an antirepressor at the tcpA promoter, we investigated expression levels in strains harboring wild-type or mutant copies of hns and ihfA. Cultures of the tcpA-lacZ strains MBN135 (wild type), GK648 (ihfA::kan), MBN148 (Δhns), and ES42 (ihfA::kan Δhns) were grown overnight in LB with a starting pH of 6.5 at 30°C, and β-galactosidase activity was measured. As was previously described by Nye et al. (43), the level of tcpA-lacZ expression in the absence of hns (MBN148) was increased about 1.5-fold compared to the wild-type (MBN135) level (Table (Table3).3). In the absence of hns (MBN148), there was no further effect of deleting ihf on tcpA-lacZ expression, suggesting that the ihf mutation is epistatic to the hns mutation at the tcpA promoter. Furthermore, deleting hns has a much greater derepressive effect on tcpA-lacZ expression in the absence of ihfA than when ihfA is present (501% versus 145%) (Table (Table3).3). This suggests that IHF counteracts H-NS repression at tcpA.

TABLE 3.
Effect of IHF on expression of the tcpA-lacZ fusion in wild-type, hns, toxT, and hns toxT strains

In an attempt to determine if IHF-mediated activation at the tcpA promoter is ToxT dependent, we investigated expression levels in strains harboring wild-type or mutant copies of toxT and ihfA. Cultures of the tcpA-lacZ strains MBN135 (wild type), GK648 (ihfA::kan), MBN142 (ΔtoxT), and ES41 (ihfA::kan ΔtoxT) were grown overnight in LB with a starting pH of 6.5 at 30°C, and β-galactosidase activity was measured. As previously described by Hulbert and Taylor (22), there is a loss of tcpA-lacZ expression in the absence of toxT (MBN142) compared to that in a toxT-containing strain (MBN135) (Table (Table3).3). There was no further loss of tcpA-lacZ expression in the ihfA toxT double mutant (ES41) compared to that in the toxT mutant alone, suggesting that the positive effect of IHF at tcpA requires ToxT. Furthermore, there was no affect of the ihf mutant in an hns toxT background (MBN168) (Table (Table3).3). Taken together, these results suggest that the IHF effect on tcpA expression requires the presence of the repressor H-NS and the activator ToxT.

Given that toxT expression is higher in an hns mutant due to derepression (43) and that the ihf effect requires the presence of ToxT, it is possible that the level of ToxT within the cell determines the necessity for IHF at tcpA. We therefore examined the effect of overexpressing toxT in the ihfA::kan background to determine if higher levels of ToxT could overcome the role of IHF in activation. Wild-type O395 or the O395 ihfA mutant ES21, harboring an empty vector or the toxT overexpression vector pRH81, was grown with or without arabinose to regulate toxT expression. Total proteins were extracted, separated, and subjected to Western blotting. The levels of ToxT were slightly reduced in the ihfA mutant strain compared to wild-type levels when toxT was not induced from the plasmid (Fig. (Fig.7),7), consistent with Fig. Fig.2B.2B. In addition, as seen in Fig. Fig.2A,2A, there is a drastic reduction in TcpA levels in the ihfA mutant compared to wild-type levels, despite this modest difference in ToxT levels. In the wild-type strain, overexpression of toxT did not detectably increase TcpA production (Fig. (Fig.7).7). However, TcpA was restored to near-wild-type levels upon overexpression of toxT in the ihf mutant. These results suggest that if ToxT levels are sufficiently high, IHF is not essential for maximal TcpA production. ToxT levels accumulate during exponential growth but decline in stationary phase (data not shown). IHF may be necessary when ToxT levels are low (early exponential phase and stationary phase under virulence gene-inducing conditions) to facilitate ToxT binding and activation at tcpA by overcoming some H-NS repression and/or altering promoter structure to facilitate ToxT binding. Similar to E. coli IHF (1), V. cholerae IHF is produced throughout the growth curve (under both virulence-inducing and -noninducing conditions), but levels are maximal in stationary phase (data not shown). This is consistent with a role for IHF in facilitating ToxT-mediated activation of tcpA when ToxT levels are low.

FIG. 7.
Overexpression of toxT in the ihfA mutant background. Strains were grown overnight in LB medium with a starting pH of 6.5 at 30°C with shaking and with the addition of 0.1% arabinose where indicated. Western blot analysis with anti-ToxT ...

DISCUSSION

In the V. cholerae El Tor strain N16961, McLeod et al. have found that, as in E. coli and Salmonella strains (2, 33), over 100 genes are differentially regulated in an ihfA mutant (34). In the work presented here, we show that IHF positively influences the expression of virulence genes in the V. cholerae classical O395 strain. The introduction of the ihfA::kan and ihfB::gen alleles into the tcpA-lacZ (MBN135) and ctx-lacZ (KSK218) fusion strains resulted in a four- to fivefold reduction in the expression of lacZ and prevented TCP and CT production. A reduction in expression was not observed at the TcpP/ToxR-dependent toxT promoter immediately upstream of the toxT gene (Fig. (Fig.8).8). However, the observation that the levels of ToxT protein in the ihfA mutant were lower than those in the wild type suggests that IHF might exert its effects at the ToxT-dependent promoter upstream of tcpA that also influences toxT expression. A direct role for IHF at the tcpA promoter was demonstrated by the ability of the purified protein to bind to a site centered at position −162 in gel mobility shift and DNase I footprinting assays. In addition, the protein was found to bend the DNA 120°. Since IHF did not appear to bind to the ctx promoter, these results suggest that the IHF effect on ctx expression is indirect due to lowered toxT expression driven from the ToxT-dependent promoter upstream of tcpA.

A direct role for H-NS in the repression of tcpA expression has previously been described (43, 71). Here, we show direct binding of H-NS to the tcpA promoter by gel mobility shift assays and DNase I footprinting. H-NS protection covered the IHF binding site (position −162) as well as the ToxT binding site (which spans from −84 to −41) (Fig. (Fig.8A).8A). Genetic studies of tcpA-lacZ expression in strains harboring wild-type or mutant copies of ihfA, hns, or toxT showed that activation by IHF appears to occur only when both H-NS and ToxT are present; the ihfA mutation is epistatic to the hns and toxT mutations. The functional dependence of IHF on H-NS and ToxT at tcpA, along with the observed overlapping binding sites of these proteins, suggests a possible model whereby IHF functions as an antirepressor at this promoter. This is further supported by the binding studies that show that IHF can displace H-NS from the tcpA regulatory region and, once bound, occlude H-NS binding.

As proposed in Fig. Fig.8A,8A, under noninducing conditions, H-NS binds directly to the tcpA promoter covering the IHF consensus sequence at position −162 as well as the ToxT binding site (spanning from −84 to −41), thereby repressing the transcription of tcpA to -F. H-NS also appears to directly repress toxT and ctx expression (43, 71). Under inducing conditions (Fig. (Fig.8B),8B), ToxT levels from the TcpP/ToxR-dependent promoter increase due to cooperation between ToxR/S and TcpP/H in the inner membrane. Activation of the ToxT-dependent tcpA-toxT transcript is facilitated by binding of IHF to the site centered at position −162 that introduces a bend in the promoter that partially displaces H-NS from the DNA. This allows greater accessibility of ToxT to its binding site, resulting in transcriptional activation of the tcpA to -F genes as well as toxT. The subsequent increase in ToxT protein levels permits full activation of tcpA to -F and ctx expression. In the absence of IHF, we propose that under inducing conditions, the increased levels of ToxT from the TcpP/ToxR-dependent promoter are insufficient to fully overcome H-NS repression, and thus, expression of tcpA to -F, toxT, and ctx is not induced to maximal levels.

Consistent with this model is the finding that loss of the IHF protein results in a fourfold reduction in tcpA expression, whereas disruption of the IHF binding site by introduction of the Δconsensus or 4PM mutation, both of which alter IHF and H-NS binding, causes only a small reduction in tcpA expression. Because the IHF and H-NS binding sites overlap, these promoter mutations phenotypically negate each other by simultaneously decreasing tcpA expression due to a reduction in IHF-mediated activation and increasing tcpA expression due to reduced H-NS repression. The hypothesis that IHF functions as an antirepressor at the tcpA promoter is also supported by the finding that IHF is not required upon overexpression of the primary activator ToxT.

There are a number of reports of site-specific DNA-binding proteins acting as H-NS antagonists by displacing H-NS from common or adjacent binding sites. For example, H-NS is displaced by VirB binding at the icsB promoter in S. flexneri (62), LeuO binding at the ompS1 promoter in S. enterica (11), and SlyA binding to two distal SlyA/H-NS binding sites at hlyE in E. coli K-12 (31). At the yjjQ-bglJ promoter in E. coli, LeuO-induced DNA looping is proposed to prevent H-NS oligomerization along the promoter (58). Similarly, IHF may function at tcpA to displace H-NS from their overlapping binding site, and the bend introduced upon IHF binding may prevent oligomerization along the promoter. A role for IHF in overcoming H-NS repression at the early promoter (Pe) of bacteriophage Mu has already been established (63). The Pe promoter of bacteriophage Mu appears to be specifically inhibited by the binding of H-NS to the promoter region. Binding of IHF to the upstream site within the Pe promoter results in direct stimulation of the promoter and also interferes with the formation of DNA-protein complexes between H-NS and Pe, thereby counteracting H-NS repression of this promoter. IHF also alleviates H-NS repression at the virB promoter in S. flexneri (47). In this example, IHF binding does not overlap the H-NS binding site as in the case of the Pe promoter of Mu but is believed to generate a conformational change in the DNA from an upstream location that facilitates the binding of the AraC-like activator VirF, which itself overcomes H-NS repression. Similarly, ToxT appears to function, at least in part, to alleviate H-NS repression at the tcpA promoter, in addition to its role as an activator, since there is less H-NS repression of tcpA in the presence of ToxT than in its absence (1.4-fold [wild type versus Δhns] versus 4.5-fold [ΔtoxT versus ΔtoxT Δhns]).

Many bacterial pathogens have acquired virulence genes by horizontal gene transfer, and it has been suggested that gene silencing by H-NS allows the newly acquired genes to be integrated into regulatory networks, like the ToxR regulon in V. cholerae, over time without initially negatively affecting the fitness of the recipient bacterium (14). Enteric bacteria, like V. cholerae, encounter multiple environmental stimuli both inside and outside the human host. It is not surprising, therefore, that bacteria have evolved complex regulatory systems to overcome H-NS silencing and respond to a range of environmental inputs. As far as we know, the primary role of TCP and CT is in human infection. The role of the global regulators H-NS and IHF in infection has been hard to define due to their pleiotropic effects on transcription and the growth defects associated with their loss. It is likely that H-NS and IHF function to modulate the topology of the promoters on which the more specific regulators, like ToxT, can act to optimize virulence gene expression in V. cholerae. Using microarray analysis, Xu et al. observed that hns is one of the most highly expressed V. cholerae genes in vitro and in the rabbit ileal loop model of V. cholerae infection (67). Additionally, Ghosh et al. (17) reported that H-NS represses ctx and tcpA expression in vivo (17). This group saw that the in vivo expression levels of ctx and tcpA were increased in an hns mutant 8 h after infection of the rabbit ileal loop. In addition, they noted that CT production was about 2.5-fold greater in the hns mutant than in the wild-type O395 strain. These data demonstrate that H-NS is highly expressed and active as a repressor at the ctx and tcpA promoters in this in vivo model. Proper colonization most likely requires a mechanism to counteract some of this H-NS repression in order to achieve optimal virulence gene expression and cause disease. Yu and DiRita (71) showed that ToxT-mediated activations of the ctx and tcpA promoters are mechanistically distinct. At ctx, ToxT has a higher affinity for its binding site than it does at tcpA (71). However, Lee et al. have shown that during infection, maximal tcpA expression occurs before maximal ctx expression (30). This is likely due, in part, to the greater H-NS repressive effect on ctx expression than on tcpA expression (43, 71). The differential expression might also be due to the action of IHF at tcpA that could serve to lower the threshold level of ToxT that is required to activate tcpA expression despite the lower affinity of ToxT for its binding site at this promoter. Further analysis of the molecular interactions between IHF, H-NS, and ToxT at the tcpA promoter will provide additional insights into the mechanism by which these proteins interact to influence the later steps in the cascade that regulates virulence gene expression in V. cholerae.

Acknowledgments

This work was supported by grants AI039654 (to R.K.T.) and AI041558 (to K.S.) from the National Institutes of Health. E.S. is the recipient of a Training Grant award from NIH (AI007519).

We thank Steven Goodman for the anti-IHF polyclonal antibody and Stephanie Batchelet for critical reading and insight into the manuscript.

Footnotes

[down-pointing small open triangle]Published ahead of print on 2 May 2008.

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