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Laboratoire de Microbiologie et de Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse, France
Correspondence
Kaymeuang Cam
cam{at}ibcg.biotoul.fr
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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-aminobutyric acid
These authors contributed equally to this work.
Present address: Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). Following an intramolecular phosphorylation step, the sensor RcsC transfers the phosphoryl group to its cognate response regulator RcsB, via a histidine-containing phosphotransmitter (Hpt) domain protein, RcsD/YojN (Takeda et al., 2001). The Rcs system is activated by alterations of the envelope (for reviews see Majdalani & Gottesman, 2005; Francez-Charlot et al., 2005a). Most of the signalling to RcsC is mediated by the outer membrane lipoprotein RcsF with a few exceptions such as the overproduction of the membrane-associated chaperone-like protein DjlA (Castanié-Cornet et al., 2006). RcsB can be activated independently of the RcsFCD phosphorelay by interacting with an accessory cofactor, RcsA. This activation pathway allows the regulation of a subset of RcsB targets (see Majdalani & Gottesman, 2005; Francez-Charlot et al., 2005a).
Transcriptome analyses indicated that up to 2.5 % of the Escherichia coli genome might be regulated by the Rcs system (Ferrières & Clarke, 2003; Hagiwara et al., 2003; our unpublished results). Approximately half of the putative targets have no defined function. The vast majority of the remaining targets are involved in envelope composition or trafficking. The system is conserved in members of the Enterobacteriaceae, including animal and plant pathogens (see Huang et al., 2006). It has been shown to be involved in pathogenesis (Dominguez-Bernal et al., 2004; Mouslim et al., 2004; Garcia-Calderon et al., 2005; Detweiler et al., 2003; Bereswill & Geider, 1997; Tobe et al., 2005) and in the development of biofilms (Ferrières & Clarke, 2003). Although reported to be essential for recovery from chlorpromazine-induced stress (Conter et al., 2002), no role of the Rcs system in adaptation to natural environmental stress has been described yet.
E. coli, while preferring neutral pH for growth, is able to resist the extreme acidic conditions that it might encounter, for instance, while passing through the stomach. Three acid resistance (AR) systems have been identified in this organism: the AR1 system, which relies on the general stress sigma factor RpoS, the arginine-dependent acid resistance system (AR3) and the glutamate-dependent acid resistance (AR2) system, the latter being the most effective. Highlighting the importance of the AR2 system is the plethora of regulators involved in its regulation, the relative importance of each regulator depending on environmental pH and growth phase. These regulators include: two phosphorelays, EvgAS (Masuda & Church, 2002) and TorRS (Bordi et al., 2003), the stationary phase 
s-factor (De Biase et al., 1999), the global regulators Crp (Castanié-Cornet & Foster, 2001) and H-NS (Hommais et al., 2001), three AraC-like regulators, GadW (Ma et al., 2002), GadX (Shin et al., 2001) and YdeO (Masuda & Church, 2003), and the Era-like GTPase TrmE (Gong et al., 2004). Central to the AR2 system is the activity of the LuxR-like transcription regulator GadE, as most of the regulators listed target gadE expression. The purpose of this complex regulatory network is the regulation of the glutamate decarboxylase genes gadA and gadB and the glutamate : -aminobutyric acid (GABA) antiporter gene gadC. The combined activity of these three enzymes increases the intracellular pH to levels compatible with E. coli survival (see Foster, 2004 for a review).
This work shows that the basal activity of the response regulator RcsB is essential for glutamate-dependent acid resistance and reveals an intriguing relationship between the activities of GadE and RcsB. In contrast, stimulation of RcsB activity through either the RcsFCD phosphorelay pathway or the RcsA pathway lowers the acid resistance. The opposing effects of RcsB on acid resistance are both mediated through the regulation of the gadA and gadBC operons.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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. The 
gad transcriptional fusions were constructed in the cloning vector pRS550, rescued in the phage RS45 and installed as a single copy on the chromosome by lysogenization to create strains SK1593 (gadW–lacZ), SK2306 (gadAwt–lacZ) and SK2321 (gadAM–lacZ) (Simons et al., 1987). Cloning fragments were generated by PCR and cloned in the BamHI and EcoRI sites of pRS550. The gadW moiety in the gadW construct extended from –400 to +30 relative to the ATG of the gadW gene. Limits for gadAwt/M are shown in Fig. 3(a). The gadA, gadB, gadX and gadE fusions were described by Castanié-Cornet & Foster (2001) and Ma et al. (2002, 2003); the limits for gadA and gadB are shown in Fig. 3(a). The 
rcsA : : cat, rcsC : : cat and rcsF : : cat mutations were constructed as described by Datsenko & Wanner (2000). The whole ORFs were deleted and replaced by the chloramphenicol resistance (cat) gene. The constructs were checked by PCR and P1 transduced into the appropriate strains.
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. Cells were grown overnight at 37 °C in Luria–Bertani rich medium supplemented with 0.4 % glucose (LBG), then diluted 1000-fold in pre-warmed, pH 2.5, M9 medium salts containing 0.4 % glucose, supplemented or not with 1.5 mM glutamate. After 0, 2 and 4 h, serial dilutions of the cultures were spotted on regular Luria–Bertani broth (LB) plates. After overnight growth at 37 °C, survival rates were determined as the ratio between c.f.u. ml–1 at 2 or 4 h and c.f.u. ml–1 at 0 h. For each assay, control experiments (acid sensitive) were performed by challenging at pH 2.5 without glutamate (data not shown).
-Galactosidase assay.
Cells were grown in LBG at 37 °C. Unless specified, overnight cultures were diluted 1000-fold and grown for 5–10 generations, prior to addition of 500 µM IPTG. The cultures were sampled at different intervals for assay of -galactosidase activities (Miller, 1992). For the experiment presented in Table 3, overnight cultures were diluted 1 : 20 000 in fresh LBG and cultured at 37 °C with agitation until OD600 reached 0.3; they were then diluted 1 : 20 in LBG with or without 0.5 mM IPTG and after 2 h (OD600 
0.5), -galactosidase activities were measured.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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). As GadE is central to glutamate-dependent acid resistance, we investigated a possible role of the Rcs system in resistance to low pH. As shown in Fig. 1(a), the survival rate of an rcsB mutant was three orders of magnitude lower than that of the wild-type strain after 2 h of acid challenge and no surviving cells (<0.001 %) were detected after 4 h, indicating that a functional rcsB allele is required for glutamate-dependent acid resistance. The implication of RcsB in the AR2 system is specific since no effect of the rcsB mutation was observed in acid resistance assays involving the AR1 and AR3 systems (data not shown).
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), indicating that the requirement for RcsB in acid resistance is not mediated by RcsA and that under these experimental conditions, the regulation of rcsA by GadE is not pertinent. We also tested the contribution of the RcsB phosphorylation pathway (RcsFCD). As shown in Fig. 1(a), the absence of any of the genes of the phosphorelay did not affect acid resistance. Therefore, either a third RcsB activation pathway is involved or only basal RcsB activity is required for resistance to low pH.
The basal RcsB activity is required for glutamate-dependent acid resistance
To evaluate the RcsB activity under these experimental conditions, the expression of two targets of RcsB, the cps and bdm genes, was measured using lacZ transcriptional fusions with their promoters. Regulation of the cps genes by RcsB is modulated by the accessory factor RcsA (Stout et al., 1991) whereas that of the bdm gene is not (Francez-Charlot et al., 2005b). Each fusion was installed into the chromosome of the strains tested as a single copy (Simons et al., 1987). The -galactosidase activity of the fusions was monitored after overnight growth in glucose-supplemented LB broth. As shown in Fig. 2a, when the Rcs phosphorelay was activated by expression of djlA from the pSG958 plasmid, strong induction of the expression of the cps–lacZ was observed and this effect was strictly dependent on having a functional rcsB allele. A similar induction was also observed when RcsB activity was increased through the overproduction of RcsB from the pHRcsB plasmid. In contrast, in the absence of djlA- or rcsB-expressing plasmids, the activities in the wild-type and rcsB backgrounds for the cps–lacZ fusion were low (51 and 38 units, respectively) and not significantly different (P>0.05), indicating that in the wild-type strain under those growth conditions there was no significant induction of RcsB activity. The expression of the bdm–lacZ fusion was also stimulated by expressing either djlA or rcsB from plasmids, although to a lesser extent with djlA (Fig. 2a). In contrast, without these plasmids the expression of the fusion remained low, and the observation that this expression was twofold lower in the rcsB than in the wild-type backgrounds (20 and 40 units, respectively) has to be interpreted as the contribution of RcsB to the constitutive expression of bdm in the wild type strain. Altogether, these results suggest that the basal RcsB activity, i.e. the activity in uninduced growth conditions, is necessary and sufficient for development of resistance to low pH.
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). Since the gadA and gadBC operons play a crucial role in this process, we tested the expression of chromosome-inserted gadA– and gadB–lacZ fusions in the rcsB background. Table 2 and Fig. 2(b) show that the transcription of both operons is dramatically reduced at the stationary phase of growth in the rcsB mutant. This effect was complemented by a plasmid expressing a functional rcsB allele through the leaky activity of the placUV5 promoter (rcsB/pHRcsB strain in Table 2). These results indicate that the basal RcsB activity positively regulates gadA and gadBC transcription. Therefore the essential role of RcsB in acid resistance is probably the maintenance of an appropriate level of GadA and GadBC.
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also show that the increase in gadA expression during the stationary phase of growth is still observed in the rpoS background: the magnitude of the effect was in the same order as that in the wild-type background (46-fold and 100-fold in early stationary phase, and 88-fold and 172-fold in late stationary phase, respectively). Similar results were obtained with the gadB fusion (Table 2). Therefore the dramatic activation of gadAB expression is only modestly mediated by RpoS. We note that this increase during the transition from exponential to late stationary phase was significantly reduced in the rpoS rcsB double mutant (sixfold) but not totally abolished. This result indicates that, under these conditions, other factors contribute to the regulation of the gad genes.
RcsB-dependent regulation of gadABC is not mediated by the regulation of gadEWX genes
The expression of gadA and gadBC is regulated by a complex network involving notably the GadE, GadW and GadX regulators (Ma et al., 2003; see Foster, 2004). It was conceivable that the RcsB effect was mediated by one of these regulators. In order to test this possibility, the activity of chromosomal lacZ fusions to the promoters of gadE, gadW and gadX was monitored. As shown in Fig. 2(b), whereas the activation of gadA and gadB is lost in the rcsB background, no effect of this mutation on the expression of gadE– and gadX–lacZ was seen. A 25 % reduction of gadW–lacZ fusion expression was observed in the rcsB strain, leaving the possibility that RcsB might activate gadAB expression through gadW. This is however unlikely, as GadW was reported to be a negative regulator of gadAB expression (Ma et al., 2002, 2003; Tucker et al., 2003). In addition, a gadW mutant was reported to resist acid as well as a wild-type strain (Tucker et al., 2003). Altogether these results indicate that the regulation of gadABC by RcsB is not mediated through the modulation of the transcription of gadE, gadX or gadW.
Both RcsB and GadE are required for acid resistance
Although GadE, GadX and GadW are together involved in glutamate-dependent acid resistance, the requirement for GadX or GadW can be overcome by overproduction of GadE, whereas the opposite is not true. In addition, the acid induction of gadABC expression is primarily due to the acid induction of gadE transcription (Ma et al., 2003). Therefore GadE appears to be the key player in acid resistance. Strengthening the central role of GadE, Fig. 1(b) shows that the low survival rate of the gadE mutant cannot be overcome by the production of RcsB from plasmid pHRcsB. More importantly, the acid sensitivity of the rcsB mutant cannot be suppressed by overproduction of GadE from a plasmid-borne gene. Therefore both GadE and RcsB are absolutely required for glutamate-dependent acid resistance. As expected, the rcsB gadE double mutant was sensitive to acid. This sensitivity can only be suppressed when both regulators are overproduced (Fig. 1b).
Both RcsB and GadE are required for activation of gadABC expression
The expression of gadE from pGadE strongly stimulates the transcription of gadA and gadBC operons in the wild-type background, as expected from previous reports (Table 3a, MPC295 and 297). The GadE-dependent regulation requires a 20 bp GadE box located upstream of the gadA/B promoters (Castanié-Cornet & Foster, 2001, Fig. 3a). As expected, gadA– and gadB–lacZ fusions lacking sequences upstream of the GadE box were still regulated by GadE (Table 3b, SK2306), whereas the same constructs in which a single substitution was introduced into the GadE box displayed dramatically lower activity and no longer responded to GadE overproduction (gadA–lacZ fusion in Table 3b, SK2321). Interestingly, expression of the wild-type gadA/B–lacZ fusions was also lower in the rcsB background and was also unaffected by the overproduction of GadE (Table 3a, MPC303 and 305). Therefore activation of gadA/BC expression by GadE requires both the GadE box and a functional rcsB allele. This result agrees with the absence of suppression of the sensitivity of the rcsB mutant to acid by the overproduction of GadE.
Activation of the RcsCDB phosphorelay represses gadABC genes and lowers acid resistance
If RcsB positively contributes to the basal level of gadABC, one might expect that increased activity of RcsB would stimulate the expression of those genes. However, unexpectedly, expression of gadA/B–lacZ fusions in strains overproducing RcsB from plasmid pHRcsB, after addition of IPTG (0.5 mM), was dramatically lower than in the wild-type control sample, 11.2-fold and 11.6-fold for gadA–lacZ and gadB–lacZ fusions, respectively (Table 2). In addition, expression of gadE, gadW and gadX fusions was also negatively affected by the overproduction of RcsB, although to a minor extent (data not shown). Therefore the activation of RcsB has a general negative effect on the expression of the gad genes. Accordingly, under those conditions, the glutamate-dependent acid resistance of a wild-type strain decreased by 1.5 log following 4 hours of acid challenge (Fig. 1c, dark grey bars). Because this effect could be misleading due to the overproduction of RcsB beyond a physiological range, the same test was performed by activating the RcsCDB phosphorelay through the expression of djlA: an even stronger reduction of acid resistance was observed (Fig. 1c, dark grey bars). We therefore conclude that the activation of RcsB has a negative effect on acid resistance. Overproduction of the RcsB accessory cofactor RcsA also represses the expression of gadA/B, although modestly (approximately twofold; data not shown). Accordingly, under those conditions, the resistance of the strain to acid was slightly lower than that of the wild-type (50 % versus 100 %, Fig. 1c).
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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), led us to investigate a potential role of the Rcs system in acid resistance. This study has brought to light the opposing dual roles of the Rcs system in acid resistance: the basal activity of the response regulator RcsB (due to the unphosphorylated form of the protein, to the basal pool of phosphorylated forms, or to a combination of both) is absolutely required for the glutamate-dependent acid resistance system, whereas the activation of RcsB, either through the RcsCD phosphorelay or through RcsA, reduces the cell's potential to resist low pH. Both activities are mediated by the activation and repression of the expression of the glutamate decarboxylase isoenzyme genes gadA/gadB and the glutamate : GABA antiporter gene gadC. Enterobacteria such as E. coli have to cope with low pH in the gastrointestinal tract. To the best of our knowledge, this is the first report of an essential role for the Rcs system in adaptation to a pertinent environmental condition.
The stationary phase and the acid induction of gadA/B expression are primarily due to the increase in gadE expression under both conditions. Accordingly, a gadE mutant is sensitive to low pH (Ma et al., 2003; Weber et al., 2005; this study). This work shows that the activity of GadE in acid resistance is absolutely dependent on a functional rcsB allele. Since the acid sensitivity of either gadE or rcsB mutants cannot be cross-suppressed by plasmids expressing either rcsB or gadE, it is likely that GadE and RcsB act at the same step in the pathway leading to acid resistance. Acid resistance is correlated with the ability of both regulators to activate the expression of the gadA and gadBC operons during the stationary phase of growth. The activation of gadA/B expression by GadE requires a GadE-binding box upstream of the promoter (Castanié-Cornet & Foster, 2001; Ma et al., 2003). Deletion and mutation analyses of gadA/BC regulatory regions did not reveal a motif that would specifically affect RcsB-dependent activation without affecting that of GadE. This result could suggest that GadE- and RcsB-activating motifs are intimately overlapping, preventing their dissection by mutations. The observation of similarities at the sequence level between the left part of the gadA/gadB GadE boxes and the RcsAB box in the regulatory region of rcsA (Fig. 3b) might support this hypothesis. Although the functional significance of this sequence similarity needs to be experimentally tested, the observation that the GadE regulon (Hommais et al., 2004) and the RcsB regulon do not significantly overlap (Ferrières & Clarke, 2003; Hagiwara et al., 2003) nevertheless indicates that GadE does not regulate all RcsB-dependent promoters and vice versa.
This study shows that only the basal RcsB activity is essential to acid resistance. The form of the protein that contributes to this basal activity is an open issue. In Salmonella enterica serovar Typhimurium, the response regulator OmpR, independently of its cognate kinase EnvZ, is required for the stationary-phase acid tolerance response. However, OmpR still needs to be activated, probably by receiving a phosphoryl group from acetyl phosphate (Bang et al., 2000). Evidence exists that RcsB can also be activated through phosphorylation by acetyl phosphate, notably when the phosphatase activity of the sensor RcsC is missing (Fredericks et al., 2006; Majdalani et al., 2005; our unpublished data). However, in the ackA pta strain, where there is no production of acetyl phosphate, or in the rcsC ack pta triple mutant, acid resistance is maintained (data not shown). If the basal RcsB activity depends on the phosphorylated form of the protein, then a third phosphorylation pathway (parallel to those of RcsC and acetyl phosphate) must exist as already suggested by Majdalani et al. (2005) and Fredericks et al. (2006). Alternatively, the unphosphorylated form of RcsB might have a regulatory activity on its own.
The increased activity of RcsB, either by the activation of the RcsCD phosphorelay or by the overproduction of the accessory cofactor RcsA, diminishes resistance to acid. This effect is through a general negative regulation of the expression of the gad genes. While still an open issue, the role of this negative regulation might be to prevent costly runaway expression of the gad genes, or to shut off the response, once the acid stress is over. This could be crucial for the bacteria, for instance, once the gastric acid barrier is passed, in order to efficiently settle into the less acidic intestinal environment. Any of these hypotheses might then explain the reported activation of rcsA expression by GadE that leads to the activation of RcsB activity, and consequently, via a feedback loop, to the repression of the gad genes.
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ACKNOWLEDGEMENTS |
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Edited by: T. Abee
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REFERENCES |
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Received 3 July 2006;
revised 2 October 2006;
accepted 19 October 2006.
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