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Journal of Bacteriology, June 2002, p. 2925-2930, Vol. 184, No. 11
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.11.2925-2930.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Isabel Delany,1 Rino Rappuoli,1 and Vincenzo Scarlato1,2*
Department of Molecular Biology, IRIS, Chiron S.p.A., 53100 Siena,1 Department of Biology, University of Bologna, 40126 Bologna, Italy2
Received 17 December 2001/ Accepted 12 March 2002
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Because of their multiple functions in both the general stress response and in specific disease mechanisms, the H. pylori heat shock proteins are expected to be tightly regulated in their expression levels. It was recently demonstrated that transcription of the groESL, hrcA-grpE-dnaK, and cbpA-hspR-orf operons encoding the major chaperones of H. pylori is negatively regulated by HspR (17). HspR is a homologue of the repressor of the dnaK operon of Streptomyces coelicolor (2, 7). By RNA analyses and footprint experiments with purified protein preparations, we have shown that HspR represses transcription by binding to regions of 75 bp on the three chaperone gene-transcribing promoters Pgro, Phrc, and Pcbp. In an attempt to identify the environmental stresses, which induce transcription from these promoters, we subjected H. pylori cultures to both osmotic shock and thermal shock at 45°C. While the Pgro and Pcbp promoters were found to be strongly inducible by treatment with 300 mM NaCl, no induction could be observed on either promoter by incubation of cultures at 45°C, indicating that heat shock does not induce transcription from HspR-dependent promoters. Recently, however, Homuth and coworkers (8) have shown that the Pgro and Phrc promoters are strongly inducible by a mild heat shock at 42°C, suggesting that HspR can indeed mediate the transcriptional response to a sudden temperature increase. In the present work we determine in detail the transcriptional response of the three HspR-dependent promoters to different environmental stresses. We show that a temperature shift to 42°C causes a typical heat shock response at all three promoters, characterized by a fast and strong induction of transcription and a subsequent shutoff phase, whose onset is determined largely by the stability of the respective mRNAs. Treatment with 300 mM NaCl causes a similar response on both Pgro and Pcbp while transcription from Phrc is essentially unaffected under these conditions. Puromycin treatment also induced transcription from the HspR-regulated promoters, indicating that misfolded proteins represent the intracellular signal that is sensed by the transcriptional machinery.
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RNA preparation. H. pylori G27 was grown in 260 ml of modified brucella broth at 37°C to mid-log phase and then exposed to various stresses. At different time intervals after stress exposure, 25-ml samples were harvested and stored at -20°C. Cells were lysed in 3.7 ml of 100 mM Tris-HCl (pH 7.5), 2 mM Na2-EDTA, and 1% sodium dodecyl sulfate for 5 min at 95°C. After 10 min of incubation on ice in the presence of 80 mM KCl, cellular debris was removed by centrifugation at 8,000 rpm for 10 min in a JA20 rotor (Beckman). To 3.5 ml of supernatant, 4.56 g of CsCl was added, and the RNA was sedimented by centrifugation in an SW65 rotor (Beckman) for 15 to 20 h at 35,000 rpm. The RNA pellet was then resuspended in 500 µl of TE (10 mM Tris-HCl [pH 8], 1 mM Na2-EDTA), extracted once with an equal volume of phenol-chloroform (1:1), ethanol precipitated, resuspended in 200 µl of TE, reprecipitated, and stored at -20°C.
Quantification of transcripts.
Pgro- and Phrc-specific transcripts were detected by reverse transcription with oligonucleotides groS (5'-GACCCTTTCTCCTAATGGCTG) and hrcA (5'-CAAACGCATCTAACAAACTCTC) as described by Spohn and Scarlato (17). Pcbp-specific transcripts were detected by S1 nuclease mapping with a 674-bp-specific DNA probe (17). This DNA fragment was cloned into the pGem3 vector (Promega) as a PCR product with oligonucleotide pair cbp1-cbp2 (5'-attattggatccACCCCAAGACGCGCTAAAGCCC and 5'-attattgAATTCTTGGGTTAGGGGGATTTTAAGGG, capital letters indicate H. pylori sequences and underlined sequences represent the BamHI and EcoRI recognition sites, respectively) and comprises the 5' regions of the cbpA gene and the upstream open reading frame HP1023. Briefly, the DNA fragment was 5' end labeled at its EcoRI site in the presence of [
-32P]ATP (5,000 Ci/mmol; Amersham) and T4 polynucleotide kinase (New England Biolabs). Approximately 20 fmol of the labeled fragment was coprecipitated with 15 µg of total H. pylori RNA and resuspended in 20 µl of hybridization buffer (80% formamide, 60 mM Tris-Cl [pH 7.5], 400 mM NaCl, 0.4 mM EDTA). The mixture was denatured at 100°C for 3 min and then incubated at the annealing temperature of 43°C. After 16 h of incubation, 180 µl of ice-cold S1 buffer (33 mM Na-acetate [pH 5.2], 5 mM ZnSO4, 250 mM NaCl) and 1 µl of S1 nuclease (400 U/µl) were added and S1 digestion was carried out for 30 min at 37°C. Samples were then extracted once with phenol-chloroform, ethanol precipitated, resuspended in 5 µl of sequencing loading buffer, heat denatured, subjected to 6% urea polyacrylamide gel electrophoresis, autoradiographed, and exposed to a PhosphorImager (Molecular Dynamics) for radioactivity quantification. As a control experiment, the flaB transcription was assayed by primer extension with oligonucleotide flaB as described in Spohn and Scarlato (18).
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FIG. 1. Structural organization of H. pylori chaperone genes (17, 21). Grey arrow bars indicate chaperone genes, black arrow bars indicate regulatory genes (hspR and hrcA), and the white arrow bar indicates a putative helicase-like gene. Chaperone genes groES and groEL code for the HspA (Hsp10) and HspB (Hsp60) proteins (20); cbpA encodes a protein with 30% amino acid identity (in a 288-amino-acid overlap) to the cochaperone curved DNA binding protein CbpA from E. coli, a homologue of DnaJ (22); hspR encodes a regulatory protein with 46% identity (in a 91-amino-acid overlap) to HspR, the negative regulator of heat shock genes in S. coelicolor (2); the helicase-like open reading frame encodes a protein with 30% identity within 421 amino acids to a hypothetical helicase-like protein from Haemophilus influenzae; hrcA encodes a protein with 28% identity (in a 71-amino-acid overlap) to the heat-inducible transcriptional repressor HrcA from B. subtilis (23); and grpE and dnaK encode the GrpE and DnaK (Hsp70) chaperones, respectively.
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FIG. 2. Heat shock response of chaperone genes. (A) Primer extension (Pgro, Phrc) and S1 nuclease (Pcbp) analyses of H. pylori RNA extracted from cells grown at 37°C (0 min) (lane 1) or upon temperature shift to 42°C (lanes 2 to 10). The time interval at which RNA was extracted is indicated, in minutes, above each lane. The products of RNA elongation or protection by S1 nuclease are marked on the rightmost side of the autoradiography by the names of the corresponding promoters: Pgro, Phrc, and Pcbp. (B) Pattern of RNA accumulation at the indicated promoters as obtained by PhosphorImager analysis quantifications of the radioactive bands shown in panel A. It is worth mentioning that primer extensions conducted on the cbpA mRNA gave unsatisfactory results. By contrast, S1 nuclease mapping turned out to function very well in mapping both the transcription start site and the regulation of transcription upon stress conditions.
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Differences in the adaptation kinetics are largely due to differences in mRNA stabilities.
To establish whether the kinetic differences observed in the shutoff phase of transcription are consequences of a possible differential regulation of the three heat shock promoters by the HspR repressor or of regulatory events at the posttranscriptional level, we decided to estimate the half-lives of the respective mRNAs. For that purpose, H. pylori G27 cells were first exposed to a 15-min heat shock at 42°C to induce transcription and then treated with rifampin to stop transcriptional initiation. RNA was prepared before and at different time intervals after the addition of rifampin, and the amount of each specific transcript was monitored by reverse transcription and S1 nuclease mapping. Figure 3 shows that the amount of Pcbp-specific transcript decreases rapidly after rifampin treatment, with a half-life which calculates to
6 min. Phrc and Pgro transcripts on the other hand appear to be particularly stable; after 30 min of rifampin treatment, 65% of the initial amount of Phrc-specific transcript and 85% of Pgro-specific transcript can still be detected. By extrapolation, the half-lives of the Phrc and Pgro transcripts can therefore be estimated to 40 to 45 min and more than 90 min, respectively. These are unusually long half-lives. In fact, in Bacillus subtilis the groE transcript shows an estimated half-life of 5 min under heat shock and non-heat shock conditions (26).
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FIG. 3. Estimation of mRNA half-lives at 42°C. Data points represent PhosphorImager analysis quantifications of radioactive bands obtained by primer extension or protection by S1 nuclease of RNA extracted before (0 min) and after the addition of rifampin to growing cells at the indicated time intervals.
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In order to investigate whether the initial induction of transcription detected after heat shock at 42°C is in part mediated by temperature-dependent changes in mRNA stability, we also measured the half-lives of the mRNAs transcribed from Pgro and Phrc at 37°C. No significant differences could be observed in the stabilities of these mRNAs between heat shock and non-heat shock conditions (data not shown), indicating that the initial induction of transcription is solely the result of regulatory events at the level of transcription initiation.
The Pcbp and Pgro promoters are also induced by osmotic shock.
Previous work had shown that salt treatment of H. pylori cells can induce transcription from the Pcbp and Pgro promoters but not from the Phrc promoter (17). To study in more detail the transcriptional response of the three HspR-regulated promoters to a sudden increase in osmolarity, we isolated total RNA from H. pylori G27 immediately before and at different time intervals after the addition of 300 mM NaCl and assayed transcript levels as before by primer extension and S1 nuclease mapping and subsequent PhosphorImager analysis. Figure 4A shows that the Pcbp and Pgro promoters are induced rapidly after salt treatment, reaching a maximum after 10 and
30 min, respectively. As shown in Fig. 4B, the induction ratios for both promoters are similar to those found for heat shock treatment, i.e.,
6- to 7-fold for Pcbp and 5- to 6-fold for Pgro. Also, the induction kinetics resemble those observed after thermal upshift, with Pcbp starting shutoff of transcription immediately after the peak of induction and Pgro transcript levels remaining at the maximal induced level for up to 3 h after temperature upshift. In agreement with previously published results (17), no significant induction could be observed at the Phrc promoter. Transcription of this promoter remains at the basal level during the whole time course of osmotic shock treatment. Similar results have been obtained by adding 440 mM sucrose to growing cells (data not shown).
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FIG. 4. Osmotic shock response of chaperone genes. (A) Primer extension (Pgro, Phrc) and S1 nuclease (Pcbp) analyses of H. pylori RNA extracted from cells grown at 37°C (0 min) (lane 1) in normal medium or upon addition of 300 mM NaCl (lanes 2 to 10). Symbols are as described in the legend to Fig. 2. (B) Pattern of RNA accumulation at the indicated promoters as obtained by PhosphorImager analysis quantifications of the radioactive bands shown in panel A.
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FIG. 5. Transcriptional response of chaperone genes to accumulation of misfolded polypeptides. (A) Primer extension (Pgro, Phrc) and S1 nuclease (Pcbp) analyses of H. pylori RNA extracted from cells grown at 37°C (0 min) (lane 1) or upon the addition of puromycin (lanes 2 to 10). Symbols are as described in the legend to Fig. 2. (B) Pattern of RNA accumulation at the indicated promoters as obtained by PhosphorImager analysis quantifications of the radioactive bands shown in panel A.
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80 and regulated negatively by the transcriptional repressor HspR (17). Very recently, by using an in vitro selection and amplification approach, two new chromosomal binding sites of the HspR protein were identified (3). Surprisingly, these HspR binding sites are located at the 3' ends of two genes coding for predicted proteins with functions unrelated to those of chaperones. This suggests that H. pylori HspR may regulate the expression of genes encoding proteins with diverse functions. The control of transcription by HspR depends on the binding of this protein to large operators mapping to different positions surrounding the promoters (17). In addition to this regulation, the possibility that another transcriptional repressor, a homolog of the B. subtilis HrcA protein (16) encoded by the hrcA-grpE-dnaK locus, might also be involved in controlling stress response has been postulated (8, 17). Evidences that chaperone gene transcription in this system responds to an increase in salinity and temperature elevation to 42°C, but not to 45°C, have been recently reported (8, 17). In this work we determined in detail the temporal pattern of transcriptional response for the three HspR-dependent promoters to different environmental stresses. A temperature shift to 42°C causes a typical heat shock response at the Pgro, Phrc, and Pcbp promoters characterized by a fast and strong induction of transcription and a subsequent shutoff phase (Fig. 2). The initial induction is a true consequence of HspR-mediated derepression of transcription initiation, as stabilities of the different mRNAs were found to remain unchanged after temperature upshift with respect to the nonstressed situation. The absolute differences in mRNA stabilities between the three promoters appear, however, to influence the onset and temporal pattern of the adaptation phase of transcription: the Pcbp promoter, which transcribes the mRNA with the shortest half-life of the three heat shock promoters (6 min) (Fig. 3), shows the earliest onset of the shutoff phase of transcription at about 10 min after temperature upshift while the Phrc and Pgro promoters, transcribing mRNAs with significantly longer half-lives (45 and >90 min, respectively), appear to enter this phase only at later stages or not at all, respectively. Despite these differences in mRNA stabilities, however, it is reasonable to assume that at the level of transcriptional initiation, HspR-dependent repression is restored on all three promoters shortly after the initial induction of transcription. Likely, at this stage of the heat shock response, the HspR repressor begins to regain its active, repression-competent conformation, possibly aided by the action of one or more specialized molecular chaperones. In support of this hypothesis is the recent finding that the DnaK chaperone of S. coelicolor can act as a corepressor together with the HspR protein (1). In this model, a DnaK-HspR complex efficiently represses transcription under non-heat shock conditions while a sudden increase in temperature leads to the transient sequestration of DnaK by accumulating unfolded proteins, thereby freeing the HspR repressor, which thus becomes inefficient in DNA binding and transcriptional repression. The increased amounts of DnaK protein produced after this induction of transcription then lead to efficient refolding of denatured proteins and restoration of the HspR-DnaK complex, which reestablishes transcriptional repression. Although in H. pylori no indications for the existence of such a complex have been found, it is likely that DnaK or another molecular chaperone participates in regulation of the DNA binding activity of HspR. In support of this hypothesis is the fact that puromycin treatment of H. pylori cells leads to a strong and irreversible induction of transcription at all three HspR-regulated promoters (Fig. 5). This induction could be interpreted as a result of the permanent sequestration of DnaK by the puromycin-induced aberrant proteins, and the consequent irreversible loss of DNA binding activity by the HspR repressor. Under physiological conditions DnaK would therefore represent the intracellular stress sensor, which mediates the appropriate transcriptional response according to the level of misfolded proteins present in the cytoplasm. All extracellular stresses, which produce aberrant or misfolded proteins in the cytoplasm, should therefore elicit a heat shock response at the HspR-dependent promoters via titration of the DnaK protein. As shown in Fig. 4, environmental stresses different from temperature changes can indeed induce a transcriptional response at the HspR-regulated promoters. The Pcbp and Pgro promoters are strongly induced by the addition of 300 mM NaCl to the growth medium, and the kinetics of induction correspond to the ones observed under heat shock conditions.
In contrast to the Pcbp and Pgro promoters, transcription from the Phrc promoter is insensitive to osmotic shock treatment, possibly indicating that this stimulus is not sufficient to destabilize the bound protein from this operator. In support of this hypothesis is the finding that HspR binds to the Phrc-associated operator with two- and fourfold-higher affinities than the Pcbp- and Pgro-associated operators, respectively (17). Alternatively, a more complex mechanism of transcriptional control might be operating on the Phrc promoter, possibly involving HrcA, the repressor encoded by the first gene of the dnaK operon. HspR and HrcA might act as corepressors on this promoter, and this dual control might lead to a differentiation of the transcriptional response according to the environmental stimulus perceived. The involvement of a second repressor, though, also implies a second negative modulator of the heat shock response. In B. subtilis it has been shown that the GroEL chaperonin functions as a negative regulator of heat shock gene expression (13, 14). In this system, GroEL is necessary for the HrcA repressor protein to function efficiently as a repressor of the dnaK operon by maintaining HrcA in a properly folded state. We speculate that an HrcA-unknown chaperone and the HspR-DnaK systems in H. pylori are required to fine-tune chaperone gene transcription in response to a sudden change in the environmental growth condition.
This work has been supported partially by EU-TMR grant FMRX-CT980164, Chiron, MURST, and University of Bologna. I.D. is the recipient of an EU-TMR fellowship (FMRX-CT980164).
Present address: Cytos Biotechnology AG, CH 8952 Zürich-Schlieren, Switzerland. ![]()
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A-like promoter and the roles of the inverted repeat sequence (CIRCE). J. Bacteriol. 177:5427-5433.
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