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Journal of Bacteriology, November 2008, p. 7268-7274, Vol. 190, No. 21
0021-9193/08/$08.00+0 doi:10.1128/JB.00967-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Characterization of irvR, a Novel Regulator of the irvA-Dependent Pathway Required for Genetic Competence and Dextran-Dependent Aggregation in Streptococcus mutans
Guoqing Niu,1
Toshinori Okinaga,1
Lin Zhu,2
Jeffrey Banas,3
Felicia Qi,1 and
Justin Merritt1*
Department of Oral Biology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104,1
UCLA School of Dentistry, Department of Oral Biology, Los Angeles, California 90025,2
University of Iowa School of Dentistry, Department of Pediatric Dentistry, Iowa City, Iowa 522423
Received 14 July 2008/
Accepted 22 August 2008

ABSTRACT
Previous studies identified
irvA as a normally repressed but
highly inducible transcription regulator capable of repressing
mutacin I gene expression in
Streptococcus mutans. In this study,
we aimed to identify and characterize the regulator(s) responsible
for repressing the expression of
irvA. An uncharacterized open
reading frame (SMU.1398) located immediately adjacent to
irvA and annotated as a putative transcription repressor was identified
as a likely candidate. The results of mutation studies confirmed
that the expression of
irvA was greatly increased in the SMU.1398
background. Mutation of SMU.1398 ("
irvR") abolished genetic
competence and reduced the expression of the late competence
genes/operons
comEA,
comY, and
dprA without affecting the expression
of the known competence regulators
comC,
comED, or
comX. In
addition,
irvR was found to be a potent negative regulator of
dextran-dependent aggregation (DDAG) and
gbpC expression. Each
of these
irvR mutant phenotypes could be rescued with a double
mutation of
irvA or complemented by introducing a wild-type
copy of
irvR on a shuttle vector. These data indicate that the
repression of
irvA is critically dependent upon
irvR and that
irvA repression is essential for the development of genetic
competence and the proper control of DDAG in
S. mutans.

INTRODUCTION
Streptococcus mutans is a gram-positive oral commensal species
found in human dental plaque and is primarily associated with
the initiation of caries development (tooth decay) (
3,
8,
28,
30,
38,
41,
45). Certain species, such as
S. mutans, have a
much greater capacity to both excrete acidic metabolites (acidogenic)
and proliferate in an acidic environment (aciduric) and thus,
can gain a competitive advantage over nonaciduric species (
2,
29). Yet, examinations of oral plaque samples and carious lesions
have identified numerous other aciduric species (
4,
9), which
suggests that the success of
S. mutans as a dental pathogen
cannot be solely attributed to its acid tolerance. Biofilm formation,
natural competence, and bacteriocin production are also recognized
as virulence factors that are necessary for the persistence
of
S. mutans in the presence of numerous environmental stresses
and fierce interspecies competition (
2,
21,
29).
Studies of genetic factors that regulate these processes in S. mutans have found a surprising variety of genetic mutations that each affect multiple virulence factors and stress tolerances simultaneously (7, 14-18, 20, 22-24, 26, 33, 36, 39, 43). This implies that a large overlap must exist between the pathways responsible for the regulation of persistence-related abilities. For example, our laboratory and others have observed that a mutation in the S. mutans ortholog of luxS creates altered oxidative and acid stress tolerances, as well as defects in biofilm formation, natural competence, and bacteriocin (mutacin I) production. (25-27, 37, 43, 44).
Previously, our laboratory further investigated the mutacin I phenotype of the luxS mutant and identified an uncharacterized transcription regulator, which we referred to as irvA, as a mediator of the mutacin I deficiency (25). Following the deletion of luxS, this gene was found to be strongly expressed, along with the concomitant loss of mutacin I production. A luxS irvA double-deletion strain regained the ability to produce mutacin I, whereas an engineered constitutive irvA expression strain was mutacin I deficient, even in a wild-type luxS background. Thus, it was concluded that irvA was an intermediate component of the pathway responsible for the repression of mutacin I in a luxS mutant background. In addition, our laboratory and others have found that the stress-responsive gene gbpC is also induced in the luxS background (25, 37). Since gbpC expression has been found to be highly responsive to numerous environmental stresses (6, 34, 35), we had speculated that the luxS mutation may similarly trigger various stress pathways in the cell, which may account for both gbpC and irvA induction (25). Likewise, irvA induction has also been found to be associated with several other genetic mutations known to have multiple stress- and virulence-related phenotypes (40). Moreover, irvA has thus far been detected in numerous strains of S. mutans (1, 25, 42); therefore, it may be a fundamental component of the basic machinery utilized to modulate multiple virulence-associated functions required for persistence.
In the current study, we report the identification of a putative repressor which is required for preventing irvA expression. This gene, which we refer to as irvR, is also absolutely required for the development of genetic competence and the proper regulation of dextran-dependent aggregation (DDAG). Furthermore, both of these phenotypes are critically dependent upon the presence of irvA as well. Thus, irvR and irvA may form a regulatory pair that is responsible for controlling important stress responses and virulence factors and may be mediators of a variety of phenotypes found in various mutant strains of S. mutans.

MATERIALS AND METHODS
Bacterial strains, plasmids, and culture conditions.
Bacterial strains and plasmids and their relevant characteristics
are listed in Table
1.
Escherichia coli cells were grown in
Luria-Bertani (LB; Difco) medium at 37°C.
E. coli strains
carrying plasmids were selected with 100 µg ml
–1 ampicillin (Fluka), 100 µg ml
–1 kanamycin (EMD),
or 150 µg ml
–1 spectinomycin (Sigma). All
S. mutans strains were grown anaerobically (85% N
2, 10% CO
2, and 5% H
2)
at 37°C.
S. mutans strains were cultivated in either brain-heart
infusion (BHI) or Todd-Hewitt medium (Difco). For the selection
of antibiotic-resistant colonies, BHI plates were supplemented
with 800 µg ml
–1 kanamycin, 15 µg ml
–1 tetracycline (Sigma), or 900 µg ml
–1 spectinomycin.
Construction of mutants.
To study the role of
irvR in
S. mutans, we constructed an
irvR deletion mutant via double-crossover homologous recombination.
To generate the construct, two fragments corresponding to approximately
1 kb of the upstream and downstream sequences of
irvR were generated
by PCR, using
Pfu polymerase with the primer pairs irvR Up F/irvR
Up R, and irvR Dn F/irvR Dn R (Table
2). Each of the primers
incorporated restriction enzyme sites, and the PCR amplicons
were subsequently cleaved with the appropriate restriction enzymes
and cloned into pFW5. The kanamycin resistance gene
aphAIII was amplified by PCR from the plasmid pTV1-OK (
16) by using
the primers Kan F and Kan R (Table
2) and cloned into pSC-A
(Stratagene) to create pGNaa3. The kanamycin resistance gene
was excised from pGNaa3 with EcoRI and ligated in between the
irvR upstream and downstream fragments to create the plasmid
pGN01R. The plasmid was confirmed via restriction digestion
and linearized for transformation into
S. mutans UA159. For
complementation analysis, the complete
irvR open reading frame
and 250 bp of the upstream intergenic region was amplified by
PCR with irvR-c F and irvR-c R (Table
2). The addition of 5'-phosphates
to the primers with T4 polynucleotide kinase (NEB) allowed the
subsequent ligation of the PCR product to the HincII site of
pDL278 to create pGN01Rc. The
irvA irvR double deletion was
created by using a strategy similar to that for the
irvR deletion
mutant except that the fragment upstream of
irvA was obtained
from a previously cloned fragment in pCR2.1 (Invitrogen) used
for the deletion of
irvA (
25). This fragment was digested by
using restriction sites compatible to the kanamycin resistance
cassette and ligated along with the
irvR downstream fragment
as described previously (Table
2). The
gbpC mutant was constructed
by single-crossover insertion inactivation using an internal
0.5-kb fragment of
gbpC amplified by PCR with the primer pairs
gbpC F and gbpC R (Table
2). The PCR product was subcloned into
the pCR2.1 vector (Invitrogen), digested with BamHI and SalI,
and cloned into the suicide vector pFW5. The resulting plasmid,
pLZ02C, was confirmed via restriction digestion and transformed
into
S. mutans UA159. The
gbpC irvR double-mutant strain GN01RC
was obtained by transforming linearized pGN01R into the
gbpC mutant strain. All mutant derivatives of UA159 were confirmed
by PCR.
RNA extraction and quantitative real-time RT-PCR.
S. mutans UA159 and its derivatives were cultivated overnight
at 37°C. The overnight cultures were diluted 1:30 in BHI
with 0.4% bovine serum albumin in a total volume of 30 ml. The
cells were allowed to grow to an optical density at 600 nm of

0.3 and collected by centrifugation. The pellets were resuspended
in 700 µl Tris-EDTA buffer (pH 8.0) and transferred to
a 2-ml screw-cap tube containing 500 µl 0.1-mm silica
beads (Biospec). Six hundred microliters of Trizol (Sigma) was
added to the tube, vortexed, and submitted to three consecutive
30-s homogenization cycles with a FastPrep-24 system (MP Biomedicals)
set at a speed of 6.0 M/s. After homogenization, 200 µl
chloroform (Sigma) was added, and the solution was centrifuged
for 10 min at full speed. The supernatant was extracted three
times with 450 µl acidic phenol (Sigma) and 200 µl
chloroform. RNA was precipitated with isopropyl alcohol and
washed with 70% ethanol. After drying, the RNA pellet was resuspended
in 87 µl RNase-free water-10 µl 10
x DNase buffer-3
µl RNase-free DNase (Ambion). The mixture was incubated
at 37°C for 45 min. After incubation, samples were further
purified with an RNeasy spin column (Qiagen) and eluted in 30
µl RNase-free water. Five hundred nanograms of total RNA
was used for cDNA synthesis using SuperScript II (Invitrogen)
according to the manufacturer's protocol. For real-time reverse
transcription-PCR (RT-PCR), oligonucleotide primers were designed
with Primer Express 3.0 software (Applied Biosystems), which
selects primers optimized for "delta-delta threshold cycle"
(

CT) method analysis. Real-time PCR was performed using an Applied
Biosystems 7300 system, and the reaction mixtures were prepared
using Applied Biosystems Sybr green PCR master mix. Changes
in levels of gene expression were calculated automatically with
the Applied Biosystems 7300 system software using the

CT method,
which is briefly described as follows:
CT =
CT(target) –
CT(housekeeping gene);

CT =
CT1 –
CT2; the levels of change
are calculated as 2
–
CT. The 16S rRNA gene was used as
the housekeeping gene reference, and all cDNA synthesis reactions
included a replicate reaction without added reverse transcriptase
to assess genomic DNA contamination. The primers used for real-time
RT-PCR are listed in Table
2.
Transformation assay.
Genetic competence was determined by a transformation efficiency assay with genomic DNA and the E. coli-Streptococcus shuttle vector pDL278. Cells were grown as mentioned above to an optical density at 600 nm of
0.3. Genomic DNA (10 µg ml–1) or plasmid DNA (1 µg ml–1) was added to each reaction mixture, and the cultures were incubated for an additional 2 h. After the incubation, the cultures were briefly sonicated (Misonix) to disperse the cells and plated on antibiotic-containing BHI agar plates, as well as on nonselective BHI plates. Successful transformation was scored based on antibiotic resistance, and the total viable cell population was determined by counting the number of colonies growing on nonselective plates. The transformation efficiency was determined by calculating the ratio of transformants to total viable cells.
Analysis of DDAG.
The DDAG assay was performed using the BTR-G medium described by Sato et al. (34), as well as with BHI. In brief, S. mutans colonies were picked from BHI plates and incubated anaerobically in BHI broth overnight at 37°C. The cells were then diluted (1:100) into 3 ml fresh BHI or BTR-G broth. The cultures were incubated for an additional 24 h and then divided into two 1-ml portions with or without 100 µg ml–1 dextran T2000 from Leuconostoc spp. Each pair of tubes was swirled briefly, and aggregation was observed as obvious clumping and cell precipitation. Generally, DDAG was obvious within 1 to 2 min of swirling the cultures.

RESULTS
irvR is required to repress irvA transcription.
Since the results of previous studies suggested that
irvA itself
appeared to be strongly regulated at the transcriptional level,
we aimed to identify and characterize its upstream regulator(s).
Previously, we found through a BLASTP analysis of the putative
sequence of IrvA that it matched strongly to a variety of Cro
repressors from various gram-positive bacteriophages (
25). Thus,
we speculated that perhaps IrvA was itself controlled by a "CI-like"
repressor, as is also the case with numerous temperate bacteriophages.
Surprisingly, the most promising candidate was located directly
adjacent to
irvA in the genome (NCBI annotation, SMU.1398; Oralgen
annotation, SMu1275). Its predicted amino acid sequence matched
well with a variety of gram-positive bacteriophage CI repressors,
with the highest homology to the streptococcal phage EJ-1 (37%
identity; 50% similar overall). Based upon its putative role
as a transcription repressor, we surmised that this gene would
be required to maintain the low, basal-level expression of
irvA normally seen during typical growth conditions. Therefore, we
deleted SMU.1398 and measured the expression of
irvA by real-time
RT-PCR to determine whether this mutation could cause a derepression
of
irvA. As shown by the results in Fig.
1, the expression of
irvA in the SMU.1398 deletion background was increased 76-fold
over the level in the wild type and could be fully complemented
by providing a wild-type copy of SMU.1398 in
trans. As expected,
the empty shuttle vector used for complementation had no effect
upon
irvA expression in the SMU.1398 mutant (Fig.
1). Thereafter,
SMU.1398 was designated
irvR, a repressor of
irvA.
irvR is essential for the development of genetic competence.
Previously, we had determined that a
luxS mutant has a reduced
capacity for genetic competence (
27). Likewise, we had observed
a similar result in several other
irvA-inducing mutants as well
(unpublished observations). Therefore, we were curious to determine
whether
irvR could also affect genetic competence, since it
seemed to be a major regulator of
irvA expression. Interestingly,
the
irvR mutant strain was found to be severely deficient in
its genetic competence ability, as we were unable to transform
this strain after repeated attempts (Fig.
2). We also scaled
up the transformation assay by 10-fold in order to sample a
larger number of cells, but we were still unable to detect any
transformants. Thus, the transformation efficiency of the
irvR mutant was <4
x 10
–10. In addition, we assayed competence
over a range of optical densities, as well as in the presence
of added synthetic competence-stimulating peptide, and found
that the
irvR mutant remained untransformable (data not shown).
However, despite the various failed attempts to transform the
irvR mutant, we were able to fully restore the transformation
defect with a
trans-complementation of
irvR (Fig.
2). Furthermore,
since the results of our previous studies suggested that
irvA expression seemed to be correlated with reduced genetic competence,
we created a double mutant of both
irvA and
irvR to determine
whether the competence defect of the
irvR mutant could be suppressed.
As shown by the results in Fig.
2, this did appear to be the
case, which suggests that both
irvR and
irvA function in the
same pathway responsible for regulating genetic competence.
irvR affects the expression of late competence genes via irvA.
The regulation of genetic competence occurs through a well-characterized
cascade of transcriptional regulation, ultimately resulting
in the expression of numerous late competence genes required
for the uptake and recombination of transforming DNA. Given
that both
irvR and
irvA seemed to have a major role in competence
development, we were curious to determine whether the competence
defect seen in the
irvR mutant strain would also correlate with
the altered expression of any of the known competence genes.
Therefore, we tested the expression of the well-characterized
competence gene regulators
comC,
comED, and
comX, as well as
genes required during late competence, such as
comYA,
comEA,
comEB,
comFA,
cinA,
coiA,
dprA,
endA,
mecA, and
recA. Of these,
the expression levels of three late competence genes essential
for natural transformability (
comEA,
comYA, and
dprA) were significantly
reduced in the
irvR background (
P < 0.001) and rescued by
an
irvR irvA double mutation (
P < 0.01) (Fig.
3). Surprisingly,
no effect was seen upon the expression of the late competence
gene regulators
comC,
comED, and
comX (data not shown). Thus,
the
irvA-dependent pathway appears to circumvent the upstream
components of the competence cascade to affect these genes through
an alternate mechanism.
Mutation of irvR induces DDAG via gbpC.
As mentioned previously, in our prior studies of a
luxS mutant,
we had observed increased expression of
gbpC (
25), an essential
mediator of DDAG (
34,
35). Conspicuously, we had noted increased
gbpC expression in several other
irvA-inducing mutations as
well (unpublished observations). Therefore, we reasoned that
perhaps the
irvR mutant might exhibit phenotypes related to
DDAG. Upon the addition of 100 µg ml
–1 dextran T2000,
we found that the
irvR mutant strain displayed rapid aggregation,
with the cells visibly clumped and fully precipitated within
1 to 2 min (Fig.
4A). Furthermore, this phenotype appeared independent
of the growth medium, as it occurred similarly with both the
published medium for DDAG assays (BTR-G) (
35) and BHI medium.
Interestingly, this response also did not require pretreatment
with any of the environmental stress conditions normally used
to induce DDAG, such as the addition of a sub-MIC concentration
of tetracycline or heat shock (
6,
35). As expected, no aggregation
was observed in the absence of dextran (data not shown). Similar
to the competence phenotype, full complementation was observed
with the introduction of a wild-type copy of
irvR on a shuttle
plasmid, and a double mutant of
irvR and
irvA was also able
to suppress the
irvR phenotype (Fig.
4A). This suggests that
both
irvR and
irvA are components of the pathway responsible
for the DDAG phenotype. In order to further characterize this
pathway, we examined the role of
gbpC as well. Consistent with
previous suggestions of
gbpC as a mediator of DDAG, a double
mutation of
gbpC and
irvR potently suppressed the DDAG phenotype
of the
irvR mutant (Fig.
4B). As a further confirmation of this
result, we also compared the expression of
gbpC in the wild-type,
irvR mutant, and
irvR irvA double-mutant strains. In the
irvR background,
gbpC expression was significantly increased over
its level in both the wild type (
P = 0.022) and the
irvR irvA double mutant (
P = 0.018). In addition, the
irvR irvA double
mutant had
gbpC expression nearly identical to that of the wild
type (Fig.
5). These results suggest that both
irvA and
gbpC are essential mediators of the DDAG phenotype in the
irvR mutant
strain and that
irvA is apparently upstream of
gbpC in this
pathway.

DISCUSSION
In the current study, we describe a novel regulator,
irvR, which
comprises an essential portion of the upstream regulatory pathway
required for the repression of
irvA, a recently characterized
transcription regulator induced by a variety of genetic mutations
(
25,
40). Based upon our previous experience with phenotypes
associated with
irvA induction, we tested both genetic competence
and DDAG in the
irvR background. Competence was found to be
severely inhibited, whereas DDAG appeared to be hyperactive.
Both of these phenotypes could be complemented efficiently by
the introduction of a wild-type copy of
irvR on a shuttle plasmid
or by creating a double mutant of both
irvR and
irvA. These
data implicate
irvR and
irvA as forming a regulatory pair that
functions to mediate a variety of phenotypes. Based upon the
genetic data, it appears that the function of
irvR is largely
devoted to preventing
irvA transcription, whereas IrvA appears
to be the major mediator of the associated phenotypes.
Both the competence and DDAG phenotypes were associated with the altered expression of effector genes. However, given the severity of the competence phenotype, it was somewhat surprising that only a subset of competence genes/operons exhibited reduced expression. Additionally, each of the differentially expressed genes/operons in the irvR mutant has been shown to be absolutely required for genetic competence, but none appeared to be affected to an extent that might be expected for a competence-negative phenotype. There are several possible explanations for this result. First, it may be simply that the combined effect of a reduction in transcription for all of these genes is sufficient to fully disrupt genetic competence. For example, both comEA and comYA are located in operons that contain a total of at least 11 genes between them, and almost all of their individual operon components play an essential role in natural transformation (5, 27, 31). Furthermore, in the irvR irvA double-mutant strain, late competence gene expression was restored to about 60% of the wild-type level on average (Fig. 3), which seems to correlate reasonably well with the transformation efficiency seen in this strain (Fig. 2). This result may be expected if reduced competence gene transcription was the source of the transformation deficiency. Alternatively, there may be an as-yet-unrecognized level of regulation of the competence system. For example, this could occur at the level of protein-protein interaction. Indeed, the comY operon gene products are thought to form a complex with each other, as well as with additional competence proteins (10). Disruption of this complex will result in a total loss of transformability (12, 13, 27). Therefore, it may be possible that in the irvR background one or more of these interactions are disrupted. Similarly, any loss in the ability to bind exogenous DNA or to recombine transforming DNA would also result in a loss of transformability. Further studies are necessary to fully reconcile the connection between irvA and competence. However, the transcription data do suggest that the reduction in gene expression of these late competence genes is irvA dependent. Studies are currently under way to determine the scope of the IrvA regulon, which should eventually determine whether IrvA affects these genes through direct regulation of their promoters. If this is indeed the case, it may explain how these late competence genes could exhibit reduced expression without any noticeable changes in the level of expression of comC, comED, or comX. However, there are some indications that S. mutans regulates the late competence genes in a manner that differs from the Streptococcus pneumoniae paradigm (19). Therefore, an alternate possibility is that IrvA regulates an uncharacterized component of the competence cascade. Further analysis of the IrvA regulon should help to determine whether this is the case, as well as identify any additional components of the pathway between irvA and gbpC.
The data presented in this study suggest that irvR and irvA are closely associated and probably function as a regulatory pair. This is consistent with the homology both putative gene products have with the CI and Cro proteins from numerous bacteriophages. If IrvR and IrvA also function similarly to CI and Cro, we would predict that stress signals influence IrvR transcription factor activity, which would subsequently modulate the expression status of irvA. The stress hypothesis is also consistent with our observation that increased gbpC expression seems to correlate with irvA expression in various genetic backgrounds (unpublished observations). As previously mentioned, gbpC induction and DDAG in S. mutans have been shown to occur in the presence of various environmental stress conditions (6, 35). Thus, an interesting possibility is that irvA-inducing genetic mutations create stress signals in the cell and/or simulate an intracellular stress state similar to that encountered during unfavorable growth conditions. Furthermore, irvR may be one of the downstream targets of these stress-regulated pathways. Studies are currently under way to examine whether there is any evidence to support this hypothesis.

ACKNOWLEDGMENTS
We thank the laboratory of R. Burne for the
E. coli-
S. mutans shuttle plasmid pDL278.
This work was supported by an NCRR COBRE grant, P20-RR018741-05, to J.M. and an NIDCR grant, DE014757-05, to F.Q.

FOOTNOTES
* Corresponding author. Mailing address: University of Oklahoma Health Sciences Center BRC364, 975 NE 10th St., Oklahoma City, OK 73104-5419. Phone: (405) 271-2324, ext. 2. Fax: (405) 271-3603. E-mail:
justin-merritt{at}ouhsc.edu 
Published ahead of print on 29 August 2008. 

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Journal of Bacteriology, November 2008, p. 7268-7274, Vol. 190, No. 21
0021-9193/08/$08.00+0 doi:10.1128/JB.00967-08
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
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