1 Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France
2 Génopole plateau puces à ADN, URA CNRS 2185, Institut Pasteur, France
3 Unité de Bio-informatique Structurale, URA CNRS 2185, Institut Pasteur, France
Correspondence
Florence Hommais
hommais{at}univ-lyon1.fr
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ABSTRACT |
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Present address: Dynamique, Evolution et Expression des Génomes, Université Louis Pasteur, 28, rue Goethe, 67000 Strasbourg, France.
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INTRODUCTION |
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Decarboxylase activity resulting from lysine, arginine and glutamate decarboxylases were proposed to enhance growth under acid conditions by neutralizing the medium (Dilworth & Glenn, 1999; Small & Waterman, 1998
). Whereas lysine decarboxylase and arginine decarboxylase systems are widely present in enterobacteria, the glutamate decarboxylase system is present in different Gram-positive and Gram-negative bacteria living in a similar ecological niche but which have no evolutionary link such as Clostridium perfringens, Shigella flexneri or Escherichia coli (Small & Waterman, 1998
). This system consists of three genes, i.e. gadA and gadB encoding highly homologous glutamate decarboxylase isoforms and gadC encoding a putative glutamate : GABA antiporter. The gadB and gadC genes form an operon and a number of factors, including H-NS, RpoS and CRP-cAMP, are involved in the transcriptional control of gad expression (Castanie-Cornet & Foster, 2001
; De Biase et al., 1999
; Rowbury, 1997
; Rowland et al., 1984
).
Using genome-wide technologies such as transcriptome analysis (Velculescu et al., 1997), GadX was identified as a regulator of the glutamate decarboxylase genes from the AraC family in E. coli (Hommais et al., 2001
; Ma et al., 2002
). As for ToxR from Vibrio cholerae, which is an acid-induced factor and a virulence regulator, GadX has been shown to be involved in the appropriate expression of genes required for virulence of enteropathogenic E. coli (Shin et al., 2001
).
In the present work we present evidence that YhiE, renamed GadE, is a regulator involved in the regulation of several genes required in the maintenance of pH homeostasis. Several of them are grouped in a specific region of the E. coli chromosome and may constitute an ecological fitness island.
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METHODS |
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Macroarrays.
Amplification reactions were performed in 96-well plates (Perkin Elmer) in a 100 µl reaction volume containing 10 ng chromosomal DNA of E. coli, 3 mM MgCl2, 0·2 mM dNTPs (Perkin Elmer), 0·3 mM each primer (E. coli ORF mer; Sigma Genosys) and 2·6 U Expand High Fidelity (Roche). Reactions were cycled 30 times (94 °C, 15 s; 55 °C, 30 s; 68 °C, 3 min) with a final cycle of 72 °C for 10 min in a thermocycler. Normalization was performed with a foreign gene encoding the luciferase of Photinus pyralis, which was amplified and printed on nylon membranes 15 times. Amplification of each PCR product was verified on agarose gels. For array preparation, nylon membranes (Qfilter; Genetix) were soaked in 10 mM Tris/1 mM EDTA (TE), pH 7·6. The ORF-specific PCR products and controls were printed using a Qpix robot (Genetix). Immediately following spot deposition, membranes were denatured and neutralized for 15 min in 0·5 M NaOH/1·5 M NaCl, then washed three times with distilled water and stored wet at -20 °C until use.
RNA preparation.
After growth and centrifugation of bacterial cells as described previously (Hommais et al., 2001), cells were lysed and RNA was extracted by a rapid procedure using FastPrep FP120 (Bio-101) and trizol solution (Invitrogen). RNA was redissolved in 100 µl TE. To remove genomic DNA, RNA was incubated for 15 min at 37 °C with DNA-free DNase from Ambion, according to the manufacturer's recommendations, and quantified by measuring A260 and A280. RNA purity and integrity were controlled by separating a sample on an agarose gel and ensuring that mRNA, tRNA and rRNAs could be seen.
cDNA probe synthesis.
Hybridization probes were generated from 1 µg RNA and 0·5 ng luciferase mRNA from Photinus pyralis (Invitrogen) by incubating AMV reverse transcriptase (Roche) for 2 h at 42 °C following a standard cDNA synthesis procedure using [-33P]dCTP [20003000 Ci mmol-1 (74111 TBq mmol-1); New England Nuclear] as described previously (Hommais et al., 2001
); 0·5 ng luciferase-purified mRNA was added before reverse transcription for the normalization procedure. Unincorporated nucleotides were removed from labelled cDNA by gel filtration through a G-25 Sephadex column (Roche). Pre-hybridization and hybridization were carried out as described previously (Hommais et al., 2001
).
Data analysis.
Analysis of the data was performed as described previously with some modification (Hommais et al., 2001). Exposed PhosphorImager screens were scanned on a 445SI PhosphorImager (Molecular Dynamics) with a pixel size of 177 µm. The intensity of each dot on the resulting TIFF image files was measured with XDOTSREADER software (Cose) and analysed using an Excel spreadsheet. The background noise was calculated from the intensity around each dot. Dot intensity was normalized according to the mean value of the intensities of luciferase spots on each DNA array, which allowed direct comparison of the two strains.
Primer extension.
Primer extensions were performed as described previously (Soutourina et al., 1999) with the following modification. The transcription start site of gadE was determined with 10 µg RNA from BE1410 containing pDIA578 and cultivated at pH 5·5 or 7. Analysis of the hdeD gene was performed with 20 µg RNA from a strain that expressed hdeD at a high level (BE1410 containing pDIA590) cultivated at pH 7. Direct sequencing on chromosomal DNA was performed as described previously (Krin et al., 2001
).
Protein purification.
To overexpress the GadE recombinant protein, its coding sequence was amplified by PCR from genomic DNA using primers 5'-GGAATTCCATATGATTTTTCTCATGACGAA-3' and 5'-CCCCCCGGGAAAATAAGATGTGATACCC-3'. These primers introduced an NdeI cloning site at the 3' end and an XmaI site at the 5' end. The PCR product was inserted into the NdeI and XmaI sites of the pivex 2.3 MCS plasmid (Roche) giving rise to pDIA579. This introduced six histidine residues at the end of the GadE protein, which was purified as described previously (Bertin et al., 1999).
Gel mobility shift assay.
Oligonucleotides used in this study are listed in Table 2. DNA fragments were amplified by PCR using the DyNAzyme EXT kit (Finnzymes) after labelling one end with [
-32P]ATP and T4 polynucleotide kinase. PCR fragments were purified using the QIAquick PCR purification kit (Qiagen). For gel mobility shift assays, GadE was bound to the labelled DNA fragment (30 ng) in 10 mM Tris, pH 7·4, 1 mM EDTA, 1 mM DTT, 10 % glycerol, 400 µg BSA ml-1, 80 mM NaCl, 100 µg poly-dIdC ml-1 and 20 mM glutamate at room temperature for 30 min. The gel shift was visualized, after migration in a 6 % acrylamide gel in 0·5x TBE buffer and 20 mM glutamate, with a PhosphorImager (Molecular Dynamics).
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RESULTS |
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To further characterize the yhiE regulatory gene we determined its transcription start site by primer extension experiments with total RNA from hns strains cultivated at pH 7 and 5·5 with pDIA578 (Table 1, Fig. 1
). Two transcription start sites located 92 and 125 nt, respectively, upstream from the ATG start codon were identified (Fig. 1
), whereas a unique site was observed in the gadX regulatory region (Tramonti et al., 2002
). A similar result was obtained from wild-type and hns strains without pDIA578 (data not shown). A strong increase in the level of these two transcripts was observed when RNA was extracted from cells cultured at low pH (Fig. 1
) and in an hns genetic background. This is in agreement with previous transcriptome analysis of an hns mutant and under acidic conditions where transcription of yhiE and gadX were shown to be induced (Hommais et al., 2001
; Tucker et al., 2002
). Taken together, this strongly suggests that YhiE is involved in bacterial resistance to low pH and the protein was therefore renamed GadE.
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At low pH, gadE overexpression significantly induced genes that are involved in the bacterial acid response, such as gadA, hdeA, hdeB or gadX (Table 3b). Again, genes induced by the response to other stresses or encoding chaperones and proteases were also induced by gadE induction, e.g. osmC, hdeA and ycgG. Several genes involved in the biosynthesis of glutamate were induced by the overexpression of gadE, such as gltD and glnH. Strikingly, several genes involved in the biosynthesis of bacterial membrane components were also induced by gadE overexpression, for example rcsA that encodes the activator of colanic acid synthesis, and rfaG, a representative of the LPS core biosynthesis genes on our macroarrays. Moreover, several genes regulated by GadE encode proteins of unknown function. Similarity searches demonstrate that two of them are similar to type 1 fimbrial proteins YcbQ and YehA, and one of them is a potential membrane protein, YdgL.
DNA-binding properties of GadE
As mentioned in Table 3, the overexpression of gadE significantly induced the expression of genes that are involved in (i) the bacterial acid response (gadA, gadX), (ii) other stress responses or that encode chaperones (hdeA, osmC), (iii) the biosynthesis of bacterial membranes (ompC, rcsA, rfaG) and (iv) the biosynthesis of glutamate (gltD). To determine the impact of GadE in such pathways, we analysed the DNA-binding properties of GadE to the promoter region of several gene targets whose products are involved in each pathway. The regulatory region of some of them has been described in detail previously: gadA (Castanie-Cornet & Foster, 2001
; De Biase et al., 1999
), gadX (Tramonti et al., 2002
), hdeAB (Arnqvist et al., 1994
; Tucker et al., 2003
), gltBD (Wiese et al., 1997
), osmC (Bouvier et al., 1998
), rcsA (Stout, 1996
), rfaQGPSBIJYZK (Clementz, 1992
) and ompC (Norioka et al., 1986
). We characterized here the promoter region of hdeD. A single transcriptional start site located 35 nt upstream from the ATG start codon was identified as an A (Fig. 2
).
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To characterize the regulatory region of these genes we analysed their DNA denaturation properties in silico (Yeramian, 2000; Yeramian & Jones, 2003
). Remarkably, the promoter of the genes in this genomic region showed high propensities for helix disruption on DNA stability maps (plotting the probability of helix-opening along the sequence) (Fig. 4
). By comparison, the non-coding DNA in the genomic regions adjacent to the acid cluster did not display such propensities for helix disruption with significantly higher melting temperatures for the corresponding promoters (Fig. 4
). Based on the structural properties of promoters of genes from the acid cluster, these results suggest that these genes could be easily depressed, which may suggest the presence of an efficient locking mechanism to prevent untimely induction of these genes.
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DISCUSSION |
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GadE seems to play an essential role in the bacterial acid response and is an activator of acid resistance, as is the case for GadX. Previous studies have demonstrated that the transcription of both gadX and gadE are downregulated by H-NS, suggesting that their targets are both components of the H-NS regulon (Hommais et al., 2001). To elucidate the mechanism underlying this higher resistance to acid stress via GadX and/or GadE, we analysed the effect of their overexpression on gene expression focusing our attention on H-NS gene targets. This led us to elaborate DNA macroarrays containing more than 200 genes of the H-NS regulon. First, no modification of gene expression could be detected at neutral pH with the overexpression of either GadX or GadE. Consistent with this, no significant difference in gene expression at neutral pH has been observed previously in a gadX mutant strain (Tucker et al., 2003
). However, even if we could not rule out some false positives, our results showed that several genes could be identified as significantly induced at low pH, demonstrating that GadE and GadX act as transcriptional activators of genes of the H-NS regulon under acidic conditions. This could argue that both regulators have a role in cell adaptation to low pH. Under low pH conditions 30 and 19 genes were induced by overexpression of gadX and gadE, respectively, and 18 genes were induced by both regulators (GadX and GadE). In addition, gel mobility shift assays demonstrated that GadE could be autoregulated, and regulated GadX, suggesting that an indirect effect of GadE on the transcriptional control of some of the target genes identified here could not be ruled out.
A low pH environment leads to cytoplasm acidification in micro-organisms. This effect induces damages in macromolecules and results in growth arrest and bacterial lysis. To alleviate such effects and maintain pH homeostasis, bacteria have developed several mechanisms that can be divided into four steps: step 1, a cellular envelope modification to diminish ionic permeability (Benjamin & Datta, 1995; Dilworth & Glenn, 1999
); step 2, the induction of DNA repair machinery and chaperones (Bearson et al., 1997
) which results in major changes in gene expression (Dilworth & Glenn, 1999
); step 3, the development of ionic pumping systems and proton extrusion/uptake (Dilworth & Glenn, 1999
); and step 4, an indirect increase in external pH (Booth, 1985
; Dilworth & Glenn, 1999
; Small & Waterman, 1998
). By performing functional clustering analysis on GadX and GadE regulons, we have presented evidence that both GadX and GadE are activators of the global bacterial acid response involved in the general adaptation of pH homeostasis maintenance in E. coli. Indeed, the targets of these genes are involved in three of the four steps of the bacterial response to cytoplasm acidification. In addition, transcriptional analysis of gadE overexpression at low pH demonstrated the induction of more than 10 genes whose products are involved in the biosynthesis of the bacterial envelope. These various features demonstrate that GadE is involved in the activation of this first bacterial response to acid stress. Analysis of the binding properties of GadE to double-stranded DNA demonstrated a direct binding of this protein to the promoter regions of ompC, rfaQ and rcsA, suggesting that GadE plays a direct role in the transcription of these genes. These observations suggest a control of GadE on the composition of the bacterial envelope in a low pH environment.
Overexpression of both gadE and gadX induced the expression of several genes involved in the second step of the bacterial response to cytoplasmic acidification: the induction of DNA repair machinery and chaperones (Bearson et al., 1997). For example, hdeA was induced by overexpression of both gadE and gadX. This gene, along with hdeB and hdeD, was first identified as H-NS-repressed and RpoS-dependent and subsequently demonstrated to be induced by acid. Its product is a periplasmic chaperone that is presumably important for counteracting the deleterious effects of acid on periplasmic proteins by suppressing aggregation of proteins under acid conditions at pH 2. As hdeA and hdeB are transcribed together in a single operon (Arnqvist et al., 1994
), it is possible to suppose that the function of HdeB is linked to that of HdeA. hdeD, which encodes an integral membrane protein of unknown function, is located immediately downstream of hdeAB and was also induced by overexpression of both gadX and gadE (Table 3
). Gel shift experiments demonstrated that both GadX (Ma et al., 2002
) and GadE bind to the promoter region of these genes, suggesting that they play a direct role in their activation. Moreover, several genes encoding putative chaperones and proteases were also induced by overexpression of gadX or gadE, e.g. ycgG and yhcA. In addition, overexpression of gadX induced the expression of several genes encoding regulatory proteins such as YdeO, a member of the AraC/XylS transcriptional regulator family. Deletion of the ydeO structural gene has been recently demonstrated to decrease acid resistance caused by EvgA overexpression, suggesting a function in the bacterial response to an acid environment (Masuda & Church, 2002
, 2003
).
Finally, the acid resistance response in the presence of glutamate has been previously shown to induce the glutamate decarboxylase system, which was suspected to catalyse the conversion of glutamate to -aminobutyrate and maintain a near to neutral intracellular pH when cells are exposed to extreme acid conditions. This corresponds to the fourth step of the E. coli response to cytoplasm acidification, i.e. the indirect external pH increase. GadX has been previously demonstrated to be involved in the transcriptional activation of the glutamate decarboxylase system (gadA/B, gadC) as a direct activator of these genes, which were up-regulated by overexpression of gadX (Hommais et al., 2001
; Ma et al., 2002
; Tramonti et al., 2002
). These genes encode two glutamate decarboxylase isoenzymes and the putative glutamate antiporter. Gel shift assays demonstrated the binding of the GadX protein to gadA and gadW promoter regions, suggesting direct control of GadX in the regulation of these genes (Ma et al., 2002
; Tramonti et al., 2002
; Tucker et al., 2003
). As for gadX, gadE is involved in the regulation of gadA. Our gel shift experiments showed a direct binding of this protein to the regulatory region of gadA, indicating that GadE may be an activator of this system. The existence of additional positive regulators involved in the transcriptional tuning of the gad system has been proposed previously (Tramonti et al., 2002
). Our results strongly suggest that GadE is such an additional positive regulator. Remarkably, overexpression of gadX induced expression of glnH, glnK, asnB and ybaS, which encodes a putative glutaminase, although no direct binding to the promoter regions of these genes could be demonstrated (data not shown). Similarly, overexpression of gadE induced expression of glnH and gltD. This acid induction of genes involved in the formation of glutamate from glutamine points to a mechanism for the endogenous formation of glutamate in conjunction with glutamate-dependent acid resistance, which has been suspected (Tucker et al., 2002
). Interestingly, GadE binds the gltBD promoter, suggesting a direct effect of this protein in the regulation of glutamate biosynthesis under acid conditions.
No consensus sequence for the binding of GadE on DNA could be identified. Therefore, the intergenic regions of the target genes were analysed in silico. Most promoter regions showed a high propensity to DNA double helix disruption, suggesting that these genes may be easily transcribed and need a very efficient locking mechanism to prevent any possible untimely induction of these genes under inappropriate conditions. Indeed, their transcription is regulated by at least three regulatory proteins: GadX, GadE and H-NS. This points out the complexity of the regulatory mechanism of the bacterial acid response, which makes E. coli highly adapted to situations that can lead to lethal acid stress. Moreover, as H-NS has been previously demonstrated to bind AT-rich DNA, which correlates well with a high DNA melting capacity, we hypothesize that the locking mechanism of acid genes is due to H-NS. Remarkably, seven of these genes, i.e. hdeB, hdeA, hdeD, gadE, gadW, gadX and gadA, are localized in the same E. coli chromosomal region between 3650 and 3665·2 kb. Most of them are induced by low pH (Tucker et al., 2002), suggesting that the presence of this cluster is needed for the survival of cells grown under these conditions. Moreover, the G+C content analysis of this region showed a significantly lower proportion than the mean G+C content of the total E. coli genome. Carriage of gene clusters with (i) specific functions, (ii) different G+C content in comparison to DNA of the host chromosome and (iii) distinct genetic units (capacity to disrupt DNA) are properties that define a fitness island (Hacker & Carniel, 2001
). Indeed, fitness islands can be considered as a component of ecological islands that enhance the adaptation of bacteria to survive or grow in their niches (Hacker & Carniel, 2001
). Such an acid fitness island could be very useful to maintain pH homeostasis of bacteria in the stomach, in the intestine or within the phagolysosomes of epithelial cells. Remarkably, a genomic comparison of E. coli strains whose genomic DNA has been completely sequenced showed that the genomic organization of this island is highly conserved in E. coli pathogenic strains O157 : H7, 2369, RS128 and CFT073, whereas this cluster could not be found in any other bacterial species. Although these comparisons require the analysis of more genomes to understand the origin of this island, our results suggest that despite a similar response to a low pH environment (Hommais et al., 2002
), bacterial species have developed specific systems to regulate genes involved in pH homeostasis.
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Received 22 July 2003;
revised 23 September 2003;
accepted 25 September 2003.