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Applied and Environmental Microbiology, June 2007, p. 3738-3741, Vol. 73, No. 11
0099-2240/07/$08.00+0 doi:10.1128/AEM.00390-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
New Insights into the Enterococcus faecalis CroRS Two-Component System Obtained Using a Differential-Display Random Arbitrarily Primed PCR Approach
Yoann Le Breton,*
Cécile Muller,
Yanick Auffray, and
Alain Rincé
Laboratoire Microbiologie de l'Environnement, EA 956, USC INRA 2017, IRBA, Université de Caen, 14032 Caen Cedex, France
Received 19 February 2007/
Accepted 27 March 2007

ABSTRACT
Using a modified random arbitrarily primed PCR approach, the
operon encoding the
Enterococcus faecalis JH2-2 CroRS two-component
regulatory system was shown to be repressed during stationary
phase, and a CroRS-regulated operon (
glnQHMP) was identified.
Gel retardation assays showed that the CroR regulator binds
specifically to the
glnQHMP promoter.

INTRODUCTION
Enterococcus faecalis has long been considered a commensal resident
of the human gastrointestinal tract, with singular capacities
to cope with and to survive severe environmental assaults (
5,
6,
8,
15). It has now been recognized as an opportunistic pathogen
capable of causing severe nosocomial infections (
7). Recent
investigations analyzing the molecular actors of
E. faecalis pathogenesis suggest that mechanisms involved in the stress
response may confer an advantage during infections (
13,
20,
21,
23,
24,
25). Although the
E. faecalis stress response proteome
has been characterized (
6), little is known about gene regulation
in response to environmental conditions. With the goal of analyzing
differential gene expression in
E. faecalis, we set up random
arbitrarily primed PCR (RAP-PCR) experiments.

RAP-PCR procedure.
E. faecalis strain JH2-2 (
29) was cultured in liquid GM17 medium
(
22), and cells were collected during mid-exponential phase
(at an optical density at 600 nm of 0.4) or entering stationary
phase. Total RNA was extracted as previously described (
16)
and used as a template for reverse transcription with a 1st
Strand cDNA synthesis kit (Roche) using the random primer Rap1
(Table
1). The resulting cDNA was purified with a QIAquick purification
kit (QIAGEN) to remove Rap1 and used as a template for PCR in
the presence of [

-
32P]dATP. For the first cycle (5 min at 94°C,
15 min at 36°C, and 1 min at 72°C), only one random
primer, Rap2 (Table
1), was added. The reaction mixture was
incubated for 5 min at 50°C, the primer Rap1 was added to
the mixture, and 30 additional cycles (30 s at 94°C, 30
s at 50°C, and 1 min at 72°C) were performed. The resulting
RAP-PCR products were purified, heat denatured, and analyzed
with a polyacrylamide sequencing gel (
18). The gel was then
transferred onto 3MM Chr paper (Whatman), dried, and exposed
to Kodak BioMax MS film. The resulting autoradiogram is presented
in Fig.
1A.
RAP-PCR methods usually use only one random primer or a mixture
of primers to create both strands of the cDNAs (
1,
19,
26).
Identification of the RAP-PCR products then requires the additional
step of cloning the corresponding cDNA before sequencing. In
this work, by using two distinct primers, one for the synthesis
of the first strand of cDNA and the other for the second strand,
the RAP-PCR procedure allowed us to bypass the cloning step.
After precisely aligning the RAP-PCR gel and the autoradiogram,
gel plugs containing the differentially amplified RAP-PCR products
were excised and resuspended in Tris-EDTA buffer, and this mixture
was used as a template for PCR amplification using primers Rap1
and Rap2. The resulting PCR products were purified and used
as templates for DNA sequencing using the primer Rap1.

Identification of growth-dependent-expressed genes.
The gel autoradiogram presented in Fig.
1A depicts four differentially
amplified RAP-PCR products: the RAP-PCR product A1 was more
intensely amplified with RNA extracted from cells entering stationary
phase, whereas the three other RAP-PCR products, A2, A3, and
A4, were more intensely amplified with RNA from exponentially
growing cells. The RAP-PCR product A1 was identified as an internal
region of the
pyrAb gene (NCBI locus EF_1716 [
14]). As part
of the 10-cistron operon encoding enzymes for pyrimidine biosynthesis,
pyrAb encodes the large subunit of the carbamoyl-phosphate synthase.
RAP-PCR product A3 corresponds to an internal fragment of the
rplC gene (NCBI locus EF_0206 [
14]) encoding the ribosomal protein
L3. Northern hybridizations confirmed the
pyr operon induction
and the
rplC repression during stationary phase (data not shown).
These results are similar to those previously observed with
a different gram-positive bacterium,
Bacillus subtilis, which
showed
pyr operon induction and
rplC repression during stationary
phase (
4). RAP-PCR products A2 and A4 were identified as internal
segments of
croS and
croR, respectively, two genes organized
as a bicistronic operon encoding the CroRS two-component system.
CroR is an OmpR response regulator able to bind to DNA. This
regulatory system has been shown to be involved in control of
the
salB gene expression (
10,
12). SalB is a secreted protein
first identified as a major antigen expressed during human endocarditis
infection (
28) and also shown to be involved in
E. faecalis cell shape maintenance and stress response (
9,
10,
12) and in
cell adherence and biofilm formation (
11). Northern hybridizations
confirmed the higher level of
croRS mRNA during mid-exponential
growth phase than during the stationary phase (data not shown).
croRS expression has been previously tested with exponentially
growing
E. faecalis cells subjected to physicochemical treatments
(
10), and no obvious differences were observed under these conditions.
This suggested that CroRS function was not essential for the
cell's response to the presence of bile salts, hyperosmotic
challenge, acid stress, and hypo- or hyperthermic shock. Our
results show that the
croRS operon is repressed when cells enter
the stationary phase, implying that its function might be more
important during exponential growth than during stationary phase.
To gain a better comprehension of this two-component system,
we next examined the nature of the genes under CroRS control.

RAP-PCR for the analysis of the CroRS regulon.
Two additional RAP-PCR experiments were performed using RNA
from exponentially growing cells of
E. faecalis wild-type strain
JH2-2 and from the mutant strain err05 (
10), which is unable
to express CroR. For the first assay, we used the primer Rap3
(Table
1) for the synthesis of the first strand of cDNA and
the primer Rap4 (Table
1) for the second strand, whereas we
inverted the order of these two primers (i.e., use of Rap4 for
the synthesis of the first cDNA strand and Rap3 for the second
cDNA strand) for the second RAP-PCR. This led to the observation
of four RAP-PCR products, B1, B2, B3 (Fig.
1B), and C1 (Fig.
1C). These products were amplified to a higher level by using
RNA extracted from the err05 mutant than by using RNA from the
wild-type JH2-2 strain. The RAP-PCR products B2 and B3 were
identified as internal fragments of the
croR gene. Even if the
CroRS system has been shown to be subject to autoregulation
(
3,
12), we interpret our result as the consequence of an aberrant
transcription of the disrupted
croR gene from the integrated
plasmid in the mutant err05 strain. RAP-PCR product B1 was identified
as an internal segment of a gene encoding a 243-amino-acid (aa)
protein homologous to ATP-binding subunits of ABC transporters
(data not shown) such as GlnQ, the ATP-binding subunit of the
Bacillus stearothermophilus Gln/Glu ABC transporter (59% identity;
79% homology) (
27). The gene was therefore renamed
glnQ. RAP-PCR
product C1 corresponds to a gene that encodes an 825-aa protein
homologous to amino acid binding proteins of ABC transporters
(data not shown) such as GlnH, the Gln-binding subunit of the
Bacillus subtilis Gln/Glu ABC transporter (56% identity; 73%
homology) (
17). The gene was therefore renamed
glnH.

CroR is directly involved in the regulation of the gln operon.
The genes
glnQ and
glnH are located at the same locus on the
E. faecalis chromosome (Fig.
2A). Genes encoding ABC transporter
components are usually organized as an operon. Downstream of
glnH, we found two other genes encoding putative permease subunits
of an ABC transporter. These two genes were renamed
glnM and
glnP according to their homologies. Chromosome sequence analysis
identified an inverse repeat (IR) structure (where
G0 is 34.8
kcal mol
1) 173 bp downstream of
glnP. This IR is directly
followed by a stretch of T residues, suggesting that the IR
could act as a Rho-independent transcription terminator (Fig.
2A). No such structure was found in the intergenic region between
the genes
glnQ,
glnH,
glnM, and
glnP, suggesting that they might
form a four-cistron operon. Northern hybridizations using a
glnQ probe (PCR amplified using primers GlnQ1 and GlnQ2; Table
1) revealed a 3.1-kb transcript when using RNA extracted from
the wild-type
E. faecalis strain JH2-2 (data not shown). This
shows that
glnQ,
glnH,
glnM, and
glnP are likely cotranscribed
as an operon, hereafter referred to as the
gln operon.
Real-time PCR experiments performed with cDNA synthesized from
RNA extracted from exponentially growing cells of
E. faecalis JH2-2 and from the CroR-deficient err05 mutant and with oligonucleotides
p23SF, p23SR, pglnQF, and pglnQR (Table
1) revealed that the
gln transcript is 4.3 times more abundant in the err05 mutant
(Fig.
2B). This result confirmed the RAP-PCR observations and
suggested that CroRS might be involved in the repression of
the
gln operon.
Using RNA extracted from exponentially growing E. faecalis JH2-2 cells, we performed 5' rapid amplification of cDNA ends (RACE) PCR experiments, as previously described (16), and mapped the gln transcript start site (+1) at a base A localized 108 nucleotides upstream of the start codon of the glnQ open reading frame (Fig. 2A). Gel retardation assays were then performed as previously described (12) using His6-tagged CroR (His6-CroR) protein and a radiolabeled DNA fragment that contains the promoter region of the gln operon (Pgln, 299 bp) from nucleotide 143 to nucleotide +156 relative to the transcriptional start point (PCR amplified with primers Pgln1 and Pgln2; Table 1). When Pgln is incubated with different amounts of phosphorylated His6-CroR, bands with reduced mobility are observed, demonstrating that CroR binds to the Pgln promoter, since this interaction is specific (Fig. 2C). This result suggests that the CroR protein regulates transcription of the gln operon via a direct DNA binding interaction.

Conclusions.
The RAP-PCR procedure described in this work was successfully
used to characterize the modifications of
E. faecalis gene expression.
This novel RAP-PCR approach, which uses two distinct primers
for the first and second strand DNA and consequently allows
the suppression of the cloning step, rapidly led to differentially
amplified RAP-PCR product sequences of excellent quality. Consequently,
compared to conventional RAP-PCR procedures, the present method
offers the advantages of (i) a reduction of the time required
for identification of differentially expressed genes and (ii)
a reduction of the number of sequencing reactions, as only one
sequence per RAP-PCR product is needed with our procedure, while
other methods required sequencing of several clones.
We showed that during the transition from exponential growth to the beginning of the stationary phase, the pyrAb gene was induced, whereas the rplC gene and the croRS operon were repressed. The CroRS system found in E. faecalis is probably required during exponential growth as a pleiotropic regulator of genes involved in the stress response (10, 12; unpublished data) and for cell shape maintenance (12), biofilm formation (11), cell adherence (11), intrinsic ß-lactam resistance (3), and glutamine/glutamate transport.
It is interesting to note that two of the identified CroR targets, salB and glnQ, were first characterized as genes encoding antigenic determinants expressed during E. faecalis human endocarditis infections (28). Future studies examining the role of the CroRS two-component system in the E. faecalis infection process seem warranted.

ACKNOWLEDGMENTS
We greatly appreciate the technical assistance of Béatrice
Gillot and Annick Blandin. We thank Mark A. Strauch for helpful
comments on the manuscript.
This work was partially funded via predoctoral fellowships to Y.L.B. and C.M. from Ministère de la Recherche et de l'Enseignement Supérieur, INRA, and Région Basse-Normandie.

FOOTNOTES
* Corresponding author. Present address: University of Maryland, Department of Biomedical Sciences, Dental School, 650 West Baltimore Street, Baltimore, MD 21201. Phone: (410) 706-1815. Fax: (410) 706-0865. E-mail:
ylebreton{at}umaryland.edu 
Published ahead of print on 13 April 2007. 
Y.L.B. and C.M. contributed equally to this work. 

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Applied and Environmental Microbiology, June 2007, p. 3738-3741, Vol. 73, No. 11
0099-2240/07/$08.00+0 doi:10.1128/AEM.00390-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.
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